quantp: quantp.r annotate

annotate quantp.r @ 3:9c70b9a95406 draft default tip

planemo upload commit 30548b09c6490f2f1f4d953a54c114d8e895fb5a

author	galaxyp
date	Wed, 06 Feb 2019 11:35:17 -0500
parents	1b11db35d7b5
children

rev	line source
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1 #***************************************************************************************************************************************
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	2 # Functions: Start
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	3 #***************************************************************************************************************************************
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	4
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	5 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	6 # PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	7 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	8 multisample_PCA = function(df, sampleinfo_df, outfile)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	9 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	10 tempdf = df[,-1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	11 tempcol = colnames(tempdf);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	12 tempgrp = sampleinfo_df[tempcol,2];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	13 tempdf = t(tempdf) %>% as.data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	14 tempdf[is.na(tempdf)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	15 tempdf$Group = tempgrp;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	16 png(outfile, width = 6, height = 6, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	17 # bitmap(outfile, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	18 g = autoplot(prcomp(select(tempdf, -Group)), data = tempdf, colour = 'Group', size=3);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	19 saveWidget(ggplotly(g), file.path(gsub("\\.png", "\\.html", outplot)))
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	20 plot(g);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	21 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	22 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	23
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	24 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	25 # Regression and Cook's distance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	26 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	27 singlesample_regression = function(PE_TE_data,htmloutfile, append=TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	28 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	29 rownames(PE_TE_data) = PE_TE_data$PE_ID;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	30 regmodel = lm(PE_abundance~TE_abundance, data=PE_TE_data);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	31 regmodel_summary = summary(regmodel);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	32
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	33 cat("<font><h3>Linear Regression model fit between Proteome and Transcriptome data</h3></font>\n",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	34 "<p>Assuming a linear relationship between Proteome and Transcriptome data, we here fit a linear regression model.</p>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	35 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	36 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	37
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	38 cat("<tr><td>Formula</td><td>","PE_abundance~TE_abundance","</td></tr>\n",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	39 "<tr><td colspan='2' align='center'> <b>Coefficients</b></td>","</tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	40 "<tr><td>",names(regmodel$coefficients[1]),"</td><td>",regmodel$coefficients[1]," (Pvalue:", regmodel_summary$coefficients[1,4],")","</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	41 "<tr><td>",names(regmodel$coefficients[2]),"</td><td>",regmodel$coefficients[2]," (Pvalue:", regmodel_summary$coefficients[2,4],")","</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	42 "<tr><td colspan='2' align='center'> <b>Model parameters</b></td>","</tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	43 "<tr><td>Residual standard error</td><td>",regmodel_summary$sigma," (",regmodel_summary$df[2]," degree of freedom)</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	44 "<tr><td>F-statistic</td><td>",regmodel_summary$fstatistic[1]," ( on ",regmodel_summary$fstatistic[2]," and ",regmodel_summary$fstatistic[3]," degree of freedom)</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	45 "<tr><td>R-squared</td><td>",regmodel_summary$r.squared,"</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	46 "<tr><td>Adjusted R-squared</td><td>",regmodel_summary$adj.r.squared,"</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	47 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	48
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	49 cat("</table>\n", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	50
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	51 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	52 "<font color='#ff0000'><h3>Regression and diagnostics plots</h3></font>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	53 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	54
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	55 outplot = paste(outdir,"/PE_TE_lm_1.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	56 png(outplot, width = 10, height = 10, units = 'in',res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	57 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	58 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	59 plot(regmodel, 1, cex.lab=1.5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	60 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	61
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	62 suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[1]] +
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	63 geom_point(aes(text=sprintf("Residual: %.2f<br>Fitted value: %.2f<br>Gene: %s", .fitted, .resid, PE_TE_data$PE_ID)),
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	64 shape = 1, size = .1, stroke = .2) +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	65 theme_light())
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	66 saveWidget(ggplotly(g, tooltip= c("text")), file.path(gsub("\\.png", "\\.html", outplot)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	67
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	68 outplot = paste(outdir,"/PE_TE_lm_2.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	69 png(outplot,width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	70 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	71 par(mfrow=c(1,1));
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	72 g <- plot(regmodel, 2, cex.lab=1.5);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	73 ggplotly(g)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	74 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	75
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	76 suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[2]] +
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	77 geom_point(aes(text=sprintf("Standarized residual: %.2f<br>Theoretical quantile: %.2f<br>Gene: %s", .qqx, .qqy, PE_TE_data$PE_ID)),
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	78 shape = 1, size = .1) +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	79 theme_light())
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	80 saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outplot)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	81
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	82
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	83 outplot = paste(outdir,"/PE_TE_lm_5.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	84 png(outplot, width = 10, height = 10, units = 'in',res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	85 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	86 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	87 plot(regmodel, 5, cex.lab=1.5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	88 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	89
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	90 cd_cont_pos <- function(leverage, level, model) {sqrt(levellength(coef(model))(1-leverage)/leverage)}
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	91 cd_cont_neg <- function(leverage, level, model) {-cd_cont_pos(leverage, level, model)}
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	92
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	93 suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[4]] +
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	94 aes(label = PE_TE_data$PE_ID) +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	95 geom_point(aes(text=sprintf("Leverage: %.2f<br>Standardized residual: %.2f<br>Gene: %s", .hat, .stdresid, PE_TE_data$PE_ID))) +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	96 theme_light())
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	97 saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outplot)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	98
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	99 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	100
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	101 cat(
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	102 '<tr bgcolor="#7a0019"><th>', "<font color='#ffcc33'><h4>1) <u>Residuals vs Fitted plot</h4></font></u></th>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	103 '<th><font color=#ffcc33><h4>2) <u>Normal Q-Q plot of residuals</h4></font></u></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	104 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	105
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	106 cat(
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	107 '<tr><td align=center><img src="PE_TE_lm_1.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	108 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$widget_div),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	109 '</td><td align=center><img src="PE_TE_lm_2.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	110 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$widget_div),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	111 '</td></tr>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	112
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	113 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	114 '<tr><td align=center>This plot checks for linear relationship assumptions.<br>If a horizontal line is observed without any distinct patterns, it indicates a linear relationship.</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	115 '<td align=center>This plot checks whether residuals are normally distributed or not.<br>It is good if the residuals points follow the straight dashed line i.e., do not deviate much from dashed line.</td></tr></table>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	116 file = htmloutfile, append = TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	117
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	118
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	119 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	120 # Residuals data
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	121 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	122 res_all = regmodel$residuals;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	123 res_mean = mean(res_all);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	124 res_sd = sd(res_all);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	125 res_diff = (res_all-res_mean);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	126 res_zscore = res_diff/res_sd;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	127 # res_outliers = res_all[which((res_zscore > 2)\|(res_zscore < -2))]
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	128
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	129
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	130 tempind = which((res_zscore > 2)\|(res_zscore < -2));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	131 res_PE_TE_data_no_outlier = PE_TE_data[-tempind,];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	132 res_PE_TE_data_no_outlier$residuals = res_all[-tempind];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	133 res_PE_TE_data_outlier = PE_TE_data[tempind,];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	134 res_PE_TE_data_outlier$residuals = res_all[tempind];
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	135
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	136 # Save the complete table for download (influential_observations)
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	137 temp_outlier_data = data.frame(res_PE_TE_data_outlier$PE_ID, res_PE_TE_data_outlier$TE_abundance, res_PE_TE_data_outlier$PE_abundance, res_PE_TE_data_outlier$residuals)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	138 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	139 outdatafile = paste(outdir,"/PE_TE_outliers_residuals.txt", sep="", collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	140 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	141
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	142
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	143 # Save the complete table for download (non influential_observations)
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	144 temp_all_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, res_all)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	145 colnames(temp_all_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	146 outdatafile = paste(outdir,"/PE_TE_abundance_residuals.txt", sep="", collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	147 write.table(temp_all_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	148
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	149
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	150 cat('<br><h2 id="inf_obs"><font color=#ff0000>Outliers based on the residuals from regression analysis</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	151 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	152 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	153 '<tr bgcolor="#7a0019"><th colspan=2><font color=#ffcc33>Residuals from Regression</font></th></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	154 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	155 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	156
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	157 cat("<tr><td>Mean Residual value</td><td>",res_mean,"</td></tr>\n",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	158 "<tr><td>Standard deviation (Residuals)</td><td>",res_sd,"</td></tr>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	159 '<tr><td>Total outliers (Residual value > 2 standard deviation from the mean)</td><td>',length(tempind),' <font size=4>(<b><a href="PE_TE_outliers_residuals.txt" target="_blank">Download these ',length(tempind),' data points with high residual values here</a></b>)</font></td>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	160 '<tr><td colspan=2 align=center>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	161 '<font size=4>(<b><a href="PE_TE_abundance_residuals.txt" target="_blank">Download the complete residuals data here</a></b>)</font>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	162 "</td></tr>\n</table><br><br>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	163 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	164
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	165 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	166
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	167
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	168 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	169
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	170 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	171 '<tr bgcolor="#7a0019"><th><font color=#ffcc33><h4>3) <u>Residuals vs Leverage plot</h4></font></u></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	172 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	173
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	174 cat(
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	175 '<tr><td align=center><img src="PE_TE_lm_5.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	176 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$widget_div)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	177 , '</td></tr>\n',
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	178 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	179
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	180 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	181 '<tr><td align=center>This plot is useful to identify any influential cases, that is outliers or extreme values.<br>They might influence the regression results upon inclusion or exclusion from the analysis.</td></tr></table><br>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	182 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	183
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	184
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	185
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	186 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	187 # Cook's Distance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	188 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	189 cat('<hr/><h2 id="inf_obs"><font color=#ff0000>INFLUENTIAL OBSERVATIONS</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	190 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	191 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	192 '<p><b>Cook\'s distance</b> computes the influence of each data point/observation on the predicted outcome. i.e. this measures how much the observation is influencing the fitted values.<br>In general use, those observations that have a <b>Cook\'s distance > than ', cookdist_upper_cutoff,' times the mean</b> may be classified as <b>influential.</b></p>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	193 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	194
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	195 cooksd <- cooks.distance(regmodel);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	196
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	197 outplot = paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	198 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	199 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	200 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	201 plot(cooksd, main="Influential Obs. by Cook\'s distance", ylab="Cook\'s distance", xlab="Observations", type="n") # plot cooks distance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	202 sel_outlier=which(cooksd>=as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	203 sel_nonoutlier=which(cooksd<as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	204 points(sel_outlier, cooksd[sel_outlier],pch="*", cex=2, cex.lab=1.5, col="red")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	205 points(sel_nonoutlier, cooksd[sel_nonoutlier],pch="*", cex=2, cex.lab=1.5, col="black")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	206 abline(h = as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T), col="red") # add cutoff line
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	207 #text(x=1:length(cooksd)+1, y=cooksd, labels=ifelse(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T),names(cooksd),""), col="red", pos=2) # add labels
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	208 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	209
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	210 cooksd_df <- data.frame(cooksd)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	211 cooksd_df$genes <- row.names(cooksd_df)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	212 cooksd_df$index <- 1:nrow(cooksd_df)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	213 cooksd_df$colors <- "black"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	214 cutoff <- as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	215 cooksd_df[cooksd_df$cooksd > cutoff,]$colors <- "red"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	216
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	217 g <- ggplot(cooksd_df, aes(x = index, y = cooksd, label = row.names(cooksd_df), color=as.factor(colors),
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	218 text=sprintf("Gene: %s<br>Cook's Distance: %.3f", row.names(cooksd_df), cooksd))) +
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	219 ggtitle("Influential Obs. by Cook's distance") + xlab("Observations") + ylab("Cook's Distance") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	220 #xlim(0, 3000) + ylim(0, .15) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	221 scale_shape_discrete(solid=F) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	222 geom_point(size = 2, shape = 8) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	223 geom_hline(yintercept = cutoff,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	224 linetype = "dashed", color = "red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	225 scale_color_manual(values = c("black" = "black", "red" = "red")) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	226 theme_light() + theme(legend.position="none")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	227 saveWidget(ggplotly(g, tooltip= "text"), file.path(gsub("\\.png", "\\.html", outplot)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	228
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	229 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	230 '<img src="PE_TE_lm_cooksd.png" width=800 height=800>',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	231 gsub("width:500px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div),
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	232 '<br>In the above plot, observations above red line (',cookdist_upper_cutoff,' * mean Cook\'s distance) are influential. Genes that are outliers could be important. These observations influences the correlation values and regression coefficients<br><br>',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	233 file = htmloutfile, append = TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	234
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	235 tempind = which(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	236 PE_TE_data_no_outlier = PE_TE_data[-tempind,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	237 PE_TE_data_no_outlier$cooksd = cooksd[-tempind];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	238 PE_TE_data_outlier = PE_TE_data[tempind,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	239 PE_TE_data_outlier$cooksd = cooksd[tempind];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	240 a = sort(PE_TE_data_outlier$cooksd, decreasing=T, index.return=T);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	241 PE_TE_data_outlier_sorted = PE_TE_data_outlier[a$ix,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	242
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	243 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	244 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	245 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	246
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	247 # Save the complete table for download (influential_observations)
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	248 temp_outlier_data = data.frame(PE_TE_data_outlier$PE_ID, PE_TE_data_outlier$TE_abundance, PE_TE_data_outlier$PE_abundance, PE_TE_data_outlier$cooksd)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	249 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	250 outdatafile = paste(outdir,"/PE_TE_influential_observation.txt", sep="", collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	251 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	252
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	253
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	254 # Save the complete table for download (non influential_observations)
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	255 temp_no_outlier_data = data.frame(PE_TE_data_no_outlier$PE_ID, PE_TE_data_no_outlier$TE_abundance, PE_TE_data_no_outlier$PE_abundance, PE_TE_data_no_outlier$cooksd)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	256 colnames(temp_no_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	257 outdatafile = paste(outdir,"/PE_TE_non_influential_observation.txt", sep="", collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	258 write.table(temp_no_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	259
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	260
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	261 cat("<tr><td>Mean Cook\'s distance</td><td>",mean(cooksd, na.rm=T),"</td></tr>\n",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	262 "<tr><td>Total influential observations (Cook\'s distance > ",cookdist_upper_cutoff," * mean Cook\'s distance)</td><td>",length(tempind),"</td>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	263
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	264 "<tr><td>Observations with Cook\'s distance < ",cookdist_upper_cutoff," * mean Cook\'s distance</td><td>",length(which(cooksd<as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))),"</td>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	265 "</table><br><br>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	266 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	267
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	268
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	269 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	270 # Scatter plot after removal of influential points
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	271 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	272 outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	273 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	274 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	275 png(outplot, width = 10, height = 10, units = 'in', res=300);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	276 # bitmap(outplot,"png16m");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	277 suppressWarnings(g <- ggplot(PE_TE_data_no_outlier, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() +
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	278 xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	279 xlim(min_lim,max_lim) + ylim(min_lim,max_lim) +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	280 geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f",
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	281 PE_ID, TE_abundance, PE_abundance))))
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	282 suppressMessages(plot(g))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	283 suppressMessages(saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot))))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	284 dev.off();
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	285
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	286
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	287 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatterplot: Before removal</font></th><th><font color=#ffcc33>Scatterplot: After removal</font></th></tr>\n', file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	288 # Before
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	289 cat("<tr><td align=center><!--<font color='#ff0000'><h3>Scatter plot between Proteome and Transcriptome Abundance</h3></font>\n-->",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	290 '<img src="TE_PE_scatter.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	291 gsub('id="html', 'id="secondhtml"',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	292 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$widget_div)),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	293 '</td>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	294 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	295
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	296 # After
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	297 cat("<td align=center>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	298 '<img src="AbundancePlot_scatter_without_outliers.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	299 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(outplot)$widget_div),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	300
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	301 '</td></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	302 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	303 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	304
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	305
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	306 cor_result_pearson = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "pearson");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	307 cor_result_spearman = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "spearman");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	308 cor_result_kendall = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "kendall");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	309
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	310 cat('<tr><td>\n', file = htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	311 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	312 cat('</td>\n', file = htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	313
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	314
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	315 cat('<td><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Method 1</font></th><th><font color=#ffcc33>Method 2</font></th><th><font color=#ffcc33>Method 3</font></th></tr>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	316 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	317
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	318 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	319 "<tr><td>Correlation method</td><td>",cor_result_pearson$method,"</td><td>",cor_result_spearman$method,"</td><td>",cor_result_kendall$method,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	320 "<tr><td>Correlation coefficient</td><td>",cor_result_pearson$estimate,"</td><td>",cor_result_spearman$estimate,"</td><td>",cor_result_kendall$estimate,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	321 file = htmloutfile, append = TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	322 cat("</table></td></tr></table>\n", file = htmloutfile, append = TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	323
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	324
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	325
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	326 if(dim(PE_TE_data_outlier)[1]<10)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	327 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	328 tab_n_row = dim(PE_TE_data_outlier)[1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	329 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	330 tab_n_row = 10;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	331 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	332
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	333 cat("<br><br><font size=5><b><a href='PE_TE_influential_observation.txt' target='_blank'>Download the complete list of influential observations</a></b></font>    ",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	334 "<font size=5><b><a href='PE_TE_non_influential_observation.txt' target='_blank'>Download the complete list (After removing influential points)</a></b></font><br>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	335 '<br><font color="brown"><h4>Top ',as.character(tab_n_row),' Influential observations (Cook\'s distance > ',cookdist_upper_cutoff,' * mean Cook\'s distance)</h4></font>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	336 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	337
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	338 cat('<table border=1 cellspacing=0 cellpadding=5> <tr bgcolor="#7a0019">\n', sep = "",file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	339 cat("<th><font color=#ffcc33>Gene</font></th><th><font color=#ffcc33>Protein Log Fold-Change</font></th><th><font color=#ffcc33>Transcript Log Fold-Change</font></th><th><font color=#ffcc33>Cook's Distance</font></th></tr>\n",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	340 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	341
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	342
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	343 for(i in 1:tab_n_row)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	344 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	345 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	346 '<tr>','<td>',as.character(PE_TE_data_outlier_sorted[i,1]),'</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	347 '<td>',format(PE_TE_data_outlier_sorted[i,2], scientific=F),'</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	348 '<td>',PE_TE_data_outlier_sorted[i,4],'</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	349 '<td>',format(PE_TE_data_outlier_sorted[i,5], scientific=F),'</td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	350 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	351 }
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	352 cat('</table><br><br>\n',file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	353
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	354
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	355 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	356
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	357
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	358
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	359 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	360 # Heatmap
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	361 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	362 singlesample_heatmap=function(PE_TE_data, htmloutfile, hm_nclust){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	363 cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Heatmap of PE and TE abundance values (Hierarchical clustering)</font></th><th><font color=#ffcc33>Number of clusters to extract: ',hm_nclust,'</font></th></tr>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	364 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	365
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	366 hc=hclust(dist(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")])))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	367 hm_cluster = cutree(hc,k=hm_nclust);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	368
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	369 outplot = paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	370 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	371 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	372 par(mfrow=c(1,1));
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	373 hmap = heatmap.2(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	374 trace="none", cexCol=1, col=greenred(100),Colv=F,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	375 labCol=c("Proteins","Transcripts"), scale="col",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	376 hclustfun = hclust, distfun = dist);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	377
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	378 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	379
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	380
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	381 p <- d3heatmap(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]), scale = "col",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	382 dendrogram = "row", colors = greenred(100),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	383 hclustfun = hclust, distfun = dist,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	384 show_grid = FALSE)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	385 saveWidget(p, file.path(gsub("\\.png", "\\.html", outplot)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	386
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	387 cat('<tr><td align=center colspan="2">',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	388 '<img src="PE_TE_heatmap.png" width=800 height=800>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	389 gsub("width:960px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	390 '</td></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	391 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	392
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	393
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	394 temp_PE_TE_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, hm_cluster);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	395 colnames(temp_PE_TE_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cluster (Hierarchical clustering)")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	396 tempoutfile = paste(outdir,"/PE_TE_hc_clusterpoints.txt",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	397 write.table(temp_PE_TE_data, file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	398
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	399
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	400 cat('<tr><td colspan="2" align=center><font size=5><a href="PE_TE_hc_clusterpoints.txt" target="_blank"><b>Download the hierarchical cluster list</b></a></font></td></tr></table>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	401 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	402 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	403
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	404
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	405 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	406 # K-means clustering
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	407 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	408 singlesample_kmeans=function(PE_TE_data, htmloutfile, nclust){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	409 PE_TE_data_kdata = PE_TE_data;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	410 k1 = kmeans(PE_TE_data_kdata[,c("PE_abundance","TE_abundance")], nclust);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	411 outplot = paste(outdir,"/PE_TE_kmeans.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	412 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	413 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	414 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	415 scatter.smooth(PE_TE_data_kdata[,"TE_abundance"], PE_TE_data_kdata[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	416 legend(1, 95, legend=c("Cluster 1", "Line 2"), col="red", lty=1:1, cex=0.8)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	417 legend(1, 95, legend="Cluster 2", col="green", lty=1:1, cex=0.8)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	418
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	419 ind=which(k1$cluster==1);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	420 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="red", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	421 ind=which(k1$cluster==2);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	422 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="green", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	423 ind=which(k1$cluster==3);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	424 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="blue", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	425 ind=which(k1$cluster==4);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	426 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="cyan", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	427 ind=which(k1$cluster==5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	428 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="black", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	429 ind=which(k1$cluster==6);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	430 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="brown", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	431 ind=which(k1$cluster==7);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	432 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="gold", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	433 ind=which(k1$cluster==8);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	434 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="thistle", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	435 ind=which(k1$cluster==9);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	436 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="yellow", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	437 ind=which(k1$cluster==10);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	438 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="orange", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	439 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	440
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	441 # Interactive plot for k-means clustering
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	442 g <- ggplot(PE_TE_data, aes(x = TE_abundance, y = PE_abundance, label = row.names(PE_TE_data),
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	443 text=sprintf("Gene: %s<br>Transcript Abundance: %.3f<br>Protein Abundance: %.3f",
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	444 PE_ID, TE_abundance, PE_abundance),
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	445 color=as.factor(k1$cluster))) +
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	446 xlab("Transcript Abundance") + ylab("Protein Abundance") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	447 scale_shape_discrete(solid=F) + geom_smooth(method = "loess", span = 2/3) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	448 geom_point(size = 1, shape = 8) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	449 theme_light() + theme(legend.position="none")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	450 saveWidget(ggplotly(g, tooltip=c("text")), file.path(gsub("\\.png", "\\.html", outplot)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	451
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	452 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>K-mean clustering</font></th><th><font color=#ffcc33>Number of clusters: ',nclust,'</font></th></tr>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	453 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	454
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	455 tempind = order(k1$cluster);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	456 tempoutfile = paste(outdir,"/PE_TE_kmeans_clusterpoints.txt",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	457 write.table(data.frame(PE_TE_data_kdata[tempind, ], Cluster=k1$cluster[tempind]), file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	458
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	459 #paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	460 cat('<tr><td colspan="2" align=center><img src="PE_TE_kmeans.png" width=800 height=800>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	461 gsub("width:500px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div), '</td></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	462 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	463 cat('<tr><td colspan="2" align=center><font size=5><a href="PE_TE_kmeans_clusterpoints.txt" target="_blank"><b>Download the cluster list</b></a></font></td></tr></table><br><hr/>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	464 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	465
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	466 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	467
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	468 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	469 # scatter plot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	470 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	471 singlesample_scatter = function(PE_TE_data, outfile)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	472 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	473 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	474 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	475 png(outfile, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	476 # bitmap(outfile, "png16m");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	477 suppressWarnings(g <- ggplot(PE_TE_data, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() +
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	478 xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	479 xlim(min_lim,max_lim) + ylim(min_lim,max_lim) +
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	480 geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f",
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	481 PE_ID, TE_abundance, PE_abundance)),
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	482 size = .5))
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	483 suppressMessages(plot(g))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	484 suppressMessages(saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outfile))))
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	485 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	486 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	487
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	488 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	489 # Correlation table
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	490 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	491 singlesample_cor = function(PE_TE_data, htmloutfile, append=TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	492 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	493 cor_result_pearson = cor.test(PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, method = "pearson");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	494 cor_result_spearman = cor.test(PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, method = "spearman");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	495 cor_result_kendall = cor.test(PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, method = "kendall");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	496
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	497 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	498 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Method 1</font></th><th><font color=#ffcc33>Method 2</font></th><th><font color=#ffcc33>Method 3</font></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	499 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	500
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	501 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	502 "<tr><td>Correlation method</td><td>",cor_result_pearson$method,"</td><td>",cor_result_spearman$method,"</td><td>",cor_result_kendall$method,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	503 "<tr><td>Correlation coefficient</td><td>",cor_result_pearson$estimate,"</td><td>",cor_result_spearman$estimate,"</td><td>",cor_result_kendall$estimate,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	504 file = htmloutfile, append = TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	505 cat("</table>\n", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	506
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	507 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	508
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	509 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	510 # Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	511 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	512 multisample_boxplot = function(df, sampleinfo_df, outfile, fill_leg, user_xlab, user_ylab)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	513 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	514 tempdf = df[,-1, drop=FALSE];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	515 tempdf = t(tempdf) %>% as.data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	516 tempdf[is.na(tempdf)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	517 tempdf$Sample = rownames(tempdf);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	518 tempdf1 = melt(tempdf, id.vars = "Sample");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	519
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	520 if("Gene" %in% colnames(df)){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	521 tempdf1$Name = df$Gene;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	522 } else if ("Protein" %in% colnames(df)){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	523 tempdf1$Name = df$Protein;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	524 } else if ("Genes" %in% colnames(df)){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	525 tempdf1$Name = df$Genes;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	526 }
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	527
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	528 tempdf1$Group = sampleinfo_df[tempdf1$Sample,2];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	529 png(outplot, width = 6, height = 6, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	530 # bitmap(outplot, "png16m");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	531 if(fill_leg=="No"){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	532 tempdf1$Group = c("case", "control")
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	533 }
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	534
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	535 g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	536 geom_boxplot()+
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	537 labs(x=user_xlab) + labs(y=user_ylab)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	538 saveWidget(ggplotly(g), file.path(gsub("\\.png", "\\.html", outfile)))
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	539 plot(g);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	540 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	541 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	542
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	543 ## A wrapper to saveWidget which compensates for arguable BUG in
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	544 ## saveWidget which requires `file` to be in current working
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	545 ## directory.
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	546 saveWidget <- function (widget,file,...) {
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	547 wd<-getwd()
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	548 on.exit(setwd(wd))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	549 outDir<-dirname(file)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	550 file<-basename(file)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	551 setwd(outDir);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	552 htmlwidgets::saveWidget(widget,file=file,selfcontained = FALSE)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	553 }
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	554
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	555 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	556 # Mean or Median of Replicates
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	557 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	558
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	559 mergeReplicates = function(TE_df,PE_df, sampleinfo_df, method)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	560 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	561 grps = unique(sampleinfo_df[,2]);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	562
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	563 TE_df_merged <<- sapply(grps, function(x){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	564 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	565 if(length(tempsample)!=1){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	566 apply(TE_df[,tempsample],1,method);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	567 }else{
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	568 return(TE_df[,tempsample]);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	569 }
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	570 });
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	571 TE_df_merged <<- data.frame(as.character(TE_df[,1]), TE_df_merged);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	572 colnames(TE_df_merged) = c(colnames(TE_df)[1], grps);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	573
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	574 PE_df_merged <<- sapply(grps, function(x){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	575 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	576 if(length(tempsample)!=1){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	577 apply(PE_df[,tempsample],1,method);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	578 }else{
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	579 return(PE_df[,tempsample]);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	580 }
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	581 });
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	582
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	583 PE_df_merged <<- data.frame(as.character(PE_df[,1]), PE_df_merged);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	584 colnames(PE_df_merged) = c(colnames(PE_df)[1], grps);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	585
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	586 #sampleinfo_df_merged = data.frame(Sample = grps, Group = grps, stringsAsFactors = F);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	587 sampleinfo_df_merged = data.frame(Sample = grps, Group = "Group", stringsAsFactors = F);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	588
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	589 return(list(TE_df_merged = TE_df_merged, PE_df_merged = PE_df_merged, sampleinfo_df_merged = sampleinfo_df_merged));
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	590 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	591
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	592 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	593 # (T-Test or Wilcoxon ranksum test) and Volcano Plot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	594 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	595
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	596 perform_Test_Volcano = function(TE_df_data,PE_df_data,TE_df_logfold, PE_df_logfold,sampleinfo_df, method, correction_method,volc_with)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	597 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	598
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	599 PE_colnames = colnames(PE_df_data);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	600 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	601 control_ind <<- sapply(control_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	602 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	603 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	604
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	605 if(method=="mean"){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	606 #PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) t.test(x[condition_ind-1], x[control_ind-1])$p.value);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	607 PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	608 }else{
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	609 if(method=="median"){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	610 PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(wilcox.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	611 # PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	612 }
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	613 }
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	614 PE_adj_pval = p.adjust(PE_pval, method = correction_method, n = length(PE_pval))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	615
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	616
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	617 TE_colnames = colnames(TE_df_data);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	618 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	619 control_ind <<- sapply(control_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	620 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	621 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	622
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	623 if(method=="mean"){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	624 # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) t.test(x[condition_ind-1], x[control_ind-1])$p.value);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	625 TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	626 }else{
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	627 if(method=="median"){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	628 TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(wilcox.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	629 # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	630 }
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	631 }
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	632 TE_adj_pval = p.adjust(TE_pval, method = correction_method, n = length(TE_pval))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	633
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	634
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	635 PE_TE_logfold_pval = data.frame(TE_df_logfold$Gene, TE_df_logfold$LogFold, TE_pval, TE_adj_pval, PE_df_logfold$LogFold, PE_pval, PE_adj_pval);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	636 colnames(PE_TE_logfold_pval) = c("Gene", "Transcript log fold-change", "p-value (transcript)", "adj p-value (transcript)", "Protein log fold-change", "p-value (protein)", "adj p-value (protein)");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	637 outdatafile = paste(outdir,"/PE_TE_logfold_pval.txt", sep="", collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	638 write.table(PE_TE_logfold_pval, file=outdatafile, row.names=F, sep="\t", quote=F);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	639 cat("<br><br><font size=5><b><a href='PE_TE_logfold_pval.txt' target='_blank'>Download the complete fold change data here</a></b></font><br>\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	640 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	641
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	642 if(length(condition_ind)!=1)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	643 {
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	644 # Volcano Plot
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	645
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	646 if(volc_with=="adj_pval")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	647 {
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	648 PE_pval = PE_adj_pval
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	649 TE_pval = TE_adj_pval
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	650 volc_ylab = "-log10 Adjusted p-value";
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	651 }else{
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	652 if(volc_with=="pval")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	653 {
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	654 volc_ylab = "-log10 p-value";
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	655 }
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	656 }
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	657 outplot_PE = paste(outdir,"/PE_volcano.png",sep="",collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	658 png(outplot_PE, width = 10, height = 10, units = 'in', res=300);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	659 # bitmap(outplot, "png16m");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	660 par(mfrow=c(1,1));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	661
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	662 plot(PE_df_logfold$LogFold, -log10(PE_pval),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	663 xlab="log2 fold change", ylab=volc_ylab,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	664 type="n")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	665 sel <- which((PE_df_logfold$LogFold<=log(2,base=2))&(PE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	666 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="black")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	667 PE_df_logfold$color <- "black"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	668 #sel <- which((PE_df_logfold$LogFold>log(2,base=2))&(PE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	669 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	670 sel1 <- which(PE_pval<=0.05)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	671 sel=intersect(sel,sel1)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	672 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="red")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	673 PE_df_logfold[sel,]$color <- "red"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	674 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	675 sel1 <- which(PE_pval>0.05)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	676 sel=intersect(sel,sel1)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	677 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="blue")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	678 PE_df_logfold[sel,]$color <- "blue"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	679 abline(h = -log(0.05,base=10), col="red", lty=2)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	680 abline(v = log(2,base=2), col="red", lty=2)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	681 abline(v = log(0.5,base=2), col="red", lty=2)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	682 dev.off();
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	683
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	684 g <- ggplot(PE_df_logfold, aes(x = LogFold, -log10(PE_pval), color = as.factor(color),
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	685 text=sprintf("Gene: %s<br>Log2 Fold-Change: %.3f<br>-log10 p-value: %.3f<br>p-value: %.3f",
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	686 Genes, LogFold, -log10(PE_pval), PE_pval))) +
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	687 xlab("log2 fold change") + ylab("-log10 p-value") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	688 geom_point(shape=1, size = 1.5, stroke = .2) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	689 scale_color_manual(values = c("black" = "black", "red" = "red", "blue" = "blue")) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	690 geom_hline(yintercept = -log(0.05,base=10), linetype="dashed", color="red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	691 geom_vline(xintercept = log(2,base=2), linetype="dashed", color="red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	692 geom_vline(xintercept = log(0.5,base=2), linetype="dashed", color="red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	693 theme_light() + theme(legend.position="none")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	694 saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot_PE)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	695
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	696 outplot_TE = paste(outdir,"/TE_volcano.png",sep="",collapse="");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	697 png(outplot_TE, width = 10, height = 10, units = 'in', res=300);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	698 # bitmap(outplot, "png16m");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	699 par(mfrow=c(1,1));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	700
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	701 plot(TE_df_logfold$LogFold, -log10(TE_pval),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	702 xlab="log2 fold change", ylab=volc_ylab,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	703 type="n")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	704
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	705 sel <- which((TE_df_logfold$LogFold<=log(2,base=2))&(TE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	706 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="black")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	707 TE_df_logfold$color <- "black"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	708 #sel <- which((TE_df_logfold$LogFold>log(2,base=2))&(TE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	709 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	710 sel1 <- which(TE_pval<=0.05)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	711 sel=intersect(sel,sel1)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	712 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="red")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	713 TE_df_logfold[sel,]$color <- "red"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	714 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	715 sel1 <- which(TE_pval>0.05)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	716 sel=intersect(sel,sel1)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	717 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="blue")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	718 TE_df_logfold[sel,]$color <- "blue"
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	719 abline(h = -log(0.05,base=10), col="red", lty=2)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	720 abline(v = log(2,base=2), col="red", lty=2)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	721 abline(v = log(0.5,base=2), col="red", lty=2)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	722 dev.off();
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	723
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	724 g <- ggplot(TE_df_logfold, aes(x = LogFold, -log10(TE_pval), color = as.factor(color),
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	725 text=sprintf("Gene: %s<br>Log2 Fold-Change: %.3f<br>-log10 p-value: %.3f<br>p-value: %.3f",
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	726 Genes, LogFold, -log10(TE_pval), TE_pval))) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	727 xlab("log2 fold change") + ylab("-log10 p-value") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	728 geom_point(shape=1, size = 1.5, stroke = .2) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	729 scale_color_manual(values = c("black" = "black", "red" = "red", "blue" = "blue")) +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	730 geom_hline(yintercept = -log(0.05,base=10), linetype="dashed", color="red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	731 geom_vline(xintercept = log(2,base=2), linetype="dashed", color="red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	732 geom_vline(xintercept = log(0.5,base=2), linetype="dashed", color="red") +
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	733 theme_light() + theme(legend.position="none")
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	734 saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot_TE)))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	735
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	736
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	737 cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Transcript Fold-Change</font></th><th><font color=#ffcc33>Protein Fold-Change</font></th></tr>\n', file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	738 cat("<tr><td align=center>",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	739 '<img src="TE_volcano.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	740 extractWidgetCode(outplot_TE)$widget_div,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	741 '</td>\n', file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	742 cat("<td align=center>",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	743 '<img src="PE_volcano.png" width=600 height=600>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	744 extractWidgetCode(outplot_PE)$widget_div,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	745 '</td></tr></table><br>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	746 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	747
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	748
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	749 }else{
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	750 cat('<br><br><b><font color=red>!!! No replicates found. Cannot perform test to check significance of differential expression. Thus, no Volcano plot generated !!!</font></b><br><br>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	751 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	752 }
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	753
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	754 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	755
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	756
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	757 #***************************************************************************************************************************************
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	758 # Functions: End
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	759 #***************************************************************************************************************************************
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	760
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	761
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	762 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	763 # Arguments
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	764 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	765 noargs = 12;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	766 args = commandArgs(trailingOnly = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	767 if(length(args) != noargs)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	768 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	769 stop(paste("Please check usage. Number of arguments is not equal to ",noargs,sep="",collapse=""));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	770 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	771
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	772 mode = args[1]; # "multiple" or "logfold"
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	773 method = args[2]; # "mean" or "median"
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	774 sampleinfo_file = args[3];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	775 proteome_file = args[4];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	776 transcriptome_file = args[5];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	777 correction_method = args[6];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	778 cookdist_upper_cutoff = args[7];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	779 numCluster = args[8];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	780 hm_nclust = args[9];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	781 volc_with = args[10];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	782
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	783 htmloutfile = args[11]; # html output file
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	784 outdir = args[12]; # html supporting files
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	785
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	786 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	787 # Check for file existance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	788 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	789 if(! file.exists(proteome_file))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	790 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	791 stop(paste("Proteome Data file does not exists. Path given: ",proteome_file,sep="",collapse=""));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	792 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	793 if(! file.exists(transcriptome_file))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	794 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	795 stop(paste("Transcriptome Data file does not exists. Path given: ",transcriptome_file,sep="",collapse=""));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	796 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	797
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	798 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	799 # Load library
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	800 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	801 options(warn=-1);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	802
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	803 suppressPackageStartupMessages(library(dplyr));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	804 suppressPackageStartupMessages(library(data.table));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	805 suppressPackageStartupMessages(library(gplots));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	806 suppressPackageStartupMessages(library(ggplot2));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	807 suppressPackageStartupMessages(library(ggfortify));
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	808 suppressPackageStartupMessages(library(plotly));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	809 suppressPackageStartupMessages(library(d3heatmap));
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	810
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	811 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	812 # Select mode and parse experiment design file
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	813 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	814 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	815 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	816 expDesign = fread(sampleinfo_file, header = FALSE, stringsAsFactors = FALSE, sep="\t") %>% data.frame();
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	817 expDesign_cc = expDesign[1:2,];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	818
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	819 sampleinfo_df = expDesign[3:nrow(expDesign),];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	820 rownames(sampleinfo_df)=1:nrow(sampleinfo_df);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	821 colnames(sampleinfo_df) = c("Sample","Group");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	822
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	823 condition_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	824 condition_g_name = "case";
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	825 control_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	826 control_g_name = "control";
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	827 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),2] = "case";
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	828 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),2] = "control";
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	829 sampleinfo_df_orig = sampleinfo_df;
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	830 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	831
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	832 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	833 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	834 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	835 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	836
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	837 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	838 # Parse Transcriptome data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	839 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	840 TE_df_orig = fread(transcriptome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	841 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	842 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	843 TE_df = TE_df_orig[,c(colnames(TE_df_orig)[1],condition_cols,control_cols)];
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	844 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	845 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	846 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	847 TE_df = TE_df_orig;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	848 colnames(TE_df) = c("Genes", "LogFold");
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	849 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	850 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	851 # Parse Proteome data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	852 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	853 PE_df_orig = fread(proteome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	854 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	855 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	856 PE_df = PE_df_orig[,c(colnames(PE_df_orig)[1],condition_cols,control_cols)];
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	857 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	858 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	859 {
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	860 PE_df = PE_df_orig;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	861 colnames(PE_df) = c("Genes", "LogFold");
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	862 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	863
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	864 #=============================================================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	865 # Create directory structures and then set the working directory to output directory
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	866 #=============================================================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	867 if(! file.exists(outdir))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	868 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	869 dir.create(outdir);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	870 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	871 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	872 # Write initial data summary in html outfile
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	873 #===============================================================================
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	874 cat("<html><head></head><body>\n", file = htmloutfile);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	875
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	876 cat("<h1><u>QuanTP: Association between abundance ratios of transcript and protein</u></h1><hr/>\n",
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	877 "<font><h3>Input data summary</h3></font>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	878 "<ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	879 "<li>Abbreviations used: PE (Proteome data) and TE (Transcriptome data)","</li><br>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	880 "<li>Input Proteome data dimension (Row Column): ", dim(PE_df)[1]," x ", dim(PE_df)[2],"</li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	881 "<li>Input Transcriptome data dimension (Row Column): ", dim(TE_df)[1]," x ", dim(TE_df)[2],"</li></ul><hr/>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	882 file = htmloutfile, append = TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	883
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	884 cat("<h3 id=table_of_content>Table of Contents:</h3>\n",
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	885 "<ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	886 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	887 "<li><a href=#corr_data>Correlation</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	888 "<li><a href=#regression_data>Regression analysis</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	889 "<li><a href=#inf_obs>Influential observations</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	890 "<li><a href=#cluster_data>Cluster analysis</a></li></ul><hr/>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	891 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	892 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	893 # Find common samples
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	894 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	895 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	896
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	897 if(length(common_samples)==0)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	898 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	899 stop("No common samples found ");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	900 cat("<b>Please check your experiment design file. Sample names (column names) in the Transcriptome and the Proteome data do not match. </b>\n",file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	901 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	902
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	903 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	904 # Create subsets based on common samples
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	905 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	906 TE_df = select(TE_df, 1, common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	907 PE_df = select(PE_df, 1, common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	908 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	909 rownames(sampleinfo_df) = sampleinfo_df[,1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	910
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	911 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	912 # Check for number of rows similarity
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	913 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	914 if(nrow(TE_df) != nrow(PE_df))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	915 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	916 stop("Number of rows in Transcriptome and Proteome data are not same i.e. they are not paired");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	917 cat("<b>The correlation analysis expects paired TE and PE data i.e. (i)th gene/transcript of TE file should correspond to (i)th protein of PE file. In the current input provided there is mismatch in terms of number of rows of TE and PE file. Please make sure you provide paired data.</b>\n",file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	918 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	919
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	920 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	921 # Number of groups
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	922 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	923 ngrps = unique(sampleinfo_df[,2]) %>% length();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	924 grps = unique(sampleinfo_df[,2]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	925 names(grps) = grps;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	926
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	927 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	928 # Change column1 name
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	929 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	930 colnames(TE_df)[1] = "Gene";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	931 colnames(PE_df)[1] = "Protein";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	932
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	933 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	934 # Treat missing values
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	935 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	936 TE_nacount = sum(is.na(TE_df));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	937 PE_nacount = sum(is.na(PE_df));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	938
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	939 TE_df[is.na(TE_df)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	940 PE_df[is.na(PE_df)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	941
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	942 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	943 # Obtain JS/HTML lines for interactive visualization
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	944 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	945 extractWidgetCode = function(outplot){
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	946 lines <- readLines(gsub("\\.png", "\\.html", outplot))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	947 return(list(
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	948 'prescripts' = c('',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	949 gsub('script', 'script',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	950 lines[grep('<head>',lines) + 3
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	951 :grep('</head>' ,lines) - 5]),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	952 ''),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	953 'widget_div' = paste('<!--',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	954 gsub('width:100%;height:400px',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	955 'width:500px;height:500px',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	956 lines[grep(lines, pattern='html-widget')]),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	957 '-->', sep=''),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	958 'postscripts' = paste('',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	959 gsub('script', 'script',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	960 lines[grep(lines, pattern='<script type')]),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	961 '', sep='')));
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	962 }
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	963 prescripts <- list()
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	964 postscripts <- list()
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	965
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	966
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	967 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	968 # Decide based on analysis mode
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	969 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	970 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	971 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	972 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	973 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	974
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	975 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	976 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	977 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data");
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	978 lines <- extractWidgetCode(outplot)
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	979 prescripts <- c(prescripts, lines$prescripts)
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	980 postscripts <- c(postscripts, lines$postscripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	981 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	982 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	983 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	984
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	985 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	986 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	987 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance data");
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	988 lines <- extractWidgetCode(outplot)
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	989 postscripts <- c(postscripts, lines$postscripts)
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	990 cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500>', lines$widget_div,
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	991 '</td></tr></table>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	992 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	993 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	994
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	995 # TE PE scatter
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	996 PE_TE_data = data.frame(PE_df, TE_df);
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	997 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	998 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	999 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatter plot between Proteome and Transcriptome Abundance</font></th></tr>\n', file = htmloutfile, append = TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1000 singlesample_scatter(PE_TE_data, outplot);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1001 lines <- extractWidgetCode(outplot);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1002 postscripts <- c(postscripts, lines$postscripts);
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	1003 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800>', gsub('width:500px;height:500px', 'width:800px;height:800px' , lines$widget_div), '</td></tr>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1004
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1005 # TE PE Cor
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1006 cat("<tr><td align=center>", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1007 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1008 cat('<font color="red">*Note that <u>correlation</u> is <u>sensitive to outliers</u> in the data. So it is important to analyze outliers/influential observations in the data.<br> Below we use <u>Cook\'s distance based approach</u> to identify such influential observations.</font>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1009 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1010 cat('</td></table>',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1011 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1012
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1013 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1014 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1015
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1016 # TE PE Regression
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1017 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1018 postscripts <- c(postscripts, c(extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1019 extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1020 extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1021 extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts,
2 1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	1022 extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts,
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	1023 gsub('data-for="html', 'data-for="secondhtml"',
1b11db35d7b5 planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039 galaxyp parents: 1 diff changeset	1024 extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$postscripts)))
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1025
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1026 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1027 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1028
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1029 # TE PE Heatmap
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1030 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1031 lines <- extractWidgetCode(paste(outdir,"/PE_TE_heatmap.png",sep="",collapse=""))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1032 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1033 prescripts <- c(prescripts, lines$prescripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1034
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1035
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1036 # TE PE Clustering (kmeans)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1037 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1038 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_TE_kmeans.png",sep="",collapse=""))$postscripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1039
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1040 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1041 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1042 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1043 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1044 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1045
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1046 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1047 outplot = paste(outdir,"/Box_TE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1048 temp_df_te_data = data.frame(TE_df[,1], log(TE_df[,2:length(TE_df)]));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1049 colnames(temp_df_te_data) = colnames(TE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1050 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance (log)");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1051 lines <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1052 prescripts <- c(prescripts, lines$prescripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1053 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1054 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1055 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1056 "<tr><td align=center>", file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1057 cat('<img src="Box_TE_all_rep.png" width=500 height=500>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1058 lines$widget_div, '</td>', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1059
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1060 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1061 outplot = paste(outdir,"/Box_PE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1062 temp_df_pe_data = data.frame(PE_df[,1], log(PE_df[,2:length(PE_df)]));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1063 colnames(temp_df_pe_data) = colnames(PE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1064 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance (log)");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1065 lines <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1066 #prescripts <- c(prescripts, lines$prescripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1067 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1068 cat("<td align=center>", '<img src="Box_PE_all_rep.png" width=500 height=500>',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1069 lines$widget_div, '</td></tr></table>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1070
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1071 # Calc TE PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1072 outplot = paste(outdir,"/PCA_TE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1073 multisample_PCA(TE_df, sampleinfo_df, outplot);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1074 PCA_TE <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1075 postscripts <- c(postscripts, PCA_TE$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1076
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1077 # Calc PE PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1078 outplot = paste(outdir,"/PCA_PE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1079 multisample_PCA(PE_df, sampleinfo_df, outplot);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1080 PCA_PE <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1081 postscripts <- c(postscripts, PCA_PE$postscripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1082
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1083 # Replicate mode
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1084 templist = mergeReplicates(TE_df,PE_df, sampleinfo_df, method);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1085 TE_df = templist$TE_df_merged;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1086 PE_df = templist$PE_df_merged;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1087 sampleinfo_df = templist$sampleinfo_df_merged;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1088 rownames(sampleinfo_df) = sampleinfo_df[,1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1089
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1090 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1091 outplot = paste(outdir,"/Box_TE_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1092 temp_df_te_data = data.frame(TE_df[,1], log(TE_df[,2:length(TE_df)]));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1093 colnames(temp_df_te_data) = colnames(TE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1094 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Transcript Abundance (log)");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1095 lines <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1096 #prescripts <- c(prescripts, lines$prescripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1097 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1098 cat('<br><font color="#ff0000"><h3>Sample wise distribution (Box plot) after using ',method,' on replicates </h3></font><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1099 "<tr><td align=center>", '<img src="Box_TE_rep.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1100
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1101 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1102 outplot = paste(outdir,"/Box_PE_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1103 temp_df_pe_data = data.frame(PE_df[,1], log(PE_df[,2:length(PE_df)]));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1104 colnames(temp_df_pe_data) = colnames(PE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1105 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Protein Abundance (log)");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1106 lines <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1107 #prescripts <- c(prescripts, lines$prescripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1108 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1109 cat("<td align=center>", '<img src="Box_PE_rep.png" width=500 height=500>', lines$widget_div, '</td></tr></table>\n', file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1110
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1111 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1112 # Calculating log fold change and running the "single" code part
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1113 #===============================================================================
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1114
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1115 TE_df = data.frame("Genes"=TE_df[,1], "LogFold"=apply(TE_df[,c(which(colnames(TE_df)==condition_g_name),which(colnames(TE_df)==control_g_name))],1,function(x) log(x[1]/x[2],base=2)));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1116 PE_df = data.frame("Genes"=PE_df[,1], "LogFold"=apply(PE_df[,c(which(colnames(PE_df)==condition_g_name),which(colnames(PE_df)==control_g_name))],1,function(x) log(x[1]/x[2],base=2)));
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1117
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1118 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1119 # Treat missing values
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1120 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1121
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1122 TE_df[is.infinite(TE_df[,2]),2] = NA;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1123 PE_df[is.infinite(PE_df[,2]),2] = NA;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1124 TE_df[is.na(TE_df)] = 0;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1125 PE_df[is.na(PE_df)] = 0;
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1126
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1127 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1128 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1129 # Find common samples
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1130 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1131
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1132 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1133 TE_df = select(TE_df, 1, common_samples);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1134 PE_df = select(PE_df, 1, common_samples);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1135 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1136 rownames(sampleinfo_df) = sampleinfo_df[,1];
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1137
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1138 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1139 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1140 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Transcript Abundance fold-change (log2)");
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1141 lines <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1142 postscripts <- c(postscripts, lines$postscripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1143 cat('<br><font color="#ff0000"><h3>Distribution (Box plot) of log fold change </h3></font>', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1144 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1145 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1146
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1147 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1148 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1149 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Protein Abundance fold-change(log2)");
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1150 lines <- extractWidgetCode(outplot)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1151 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1152 cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500>', lines$widget_div,'</td></tr></table>\n', file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1153
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1154
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1155 # Log Fold Data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1156 perform_Test_Volcano(TE_df_orig,PE_df_orig,TE_df, PE_df,sampleinfo_df_orig,method,correction_method,volc_with)
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1157 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/TE_volcano.png",sep="",collapse=""))$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1158 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_volcano.png",sep="",collapse=""))$postscripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1159
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1160 # Print PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1161
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1162 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>PCA plot: Transcriptome data</font></th><th><font color=#ffcc33>PCA plot: Proteome data</font></th></tr>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1163 "<tr><td align=center>", '<img src="PCA_TE_all_rep.png" width=500 height=500>', PCA_TE$widget_div, '</td>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1164 "<td align=center>", '<img src="PCA_PE_all_rep.png" width=500 height=500>', PCA_PE$widget_div, '</td></tr></table>\n',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1165 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1166
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1167
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1168
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1169 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1170 file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1171
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1172 PE_TE_data = data.frame(PE_df, TE_df);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1173 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1174
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1175 # TE PE scatter
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1176 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1177 cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatter plot between Proteome and Transcriptome Abundance</font></th></tr>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1178 singlesample_scatter(PE_TE_data, outplot);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1179 lines <- extractWidgetCode(outplot);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1180 postscripts <- c(postscripts, lines$postscripts);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1181 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800>', gsub('width:500px;height:500px', 'width:800px;height:800px' , lines$widget_div),
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1182 '</td>\n', file = htmloutfile, append = TRUE);
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1183
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1184 # TE PE Cor
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1185 cat("<tr><td align=center>\n", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1186 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1187 cat('<font color="red">*Note that <u>correlation</u> is <u>sensitive to outliers</u> in the data. So it is important to analyze outliers/influential observations in the data.<br> Below we use <u>Cook\'s distance based approach</u> to identify such influential observations.</font>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1188 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1189 cat('</td></table>',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1190 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1191
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1192 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1193 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1194
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1195 # TE PE Regression
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1196 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1197 postscripts <- c(postscripts, c(extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1198 extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1199 extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1200 extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1201 extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts,
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1202 gsub('data-for="html', 'data-for="secondhtml"',
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1203 extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$postscripts)));
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1204
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1205 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1206 file = htmloutfile, append = TRUE);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1207
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1208 #TE PE Heatmap
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1209 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1210 lines <- extractWidgetCode(paste(outdir,"/PE_TE_heatmap.png",sep="",collapse=""))
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1211 postscripts <- c(postscripts, lines$postscripts)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1212 prescripts <- c(prescripts, lines$prescripts)
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1213
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1214 #TE PE Clustering (kmeans)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1215 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1216 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_TE_kmeans.png",sep="",collapse=""))$postscripts);
0 f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1217 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1218 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1219 cat("<h3>Go To:</h3>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1220 "<ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1221 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1222 "<li><a href=#corr_data>Correlation</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1223 "<li><a href=#regression_data>Regression analysis</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1224 "<li><a href=#inf_obs>Influential observations</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1225 "<li><a href=#cluster_data>Cluster analysis</a></li></ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1226 "<br><a href=#>TOP</a>",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1227 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1228 cat("</body></html>\n", file = htmloutfile, append = TRUE);
1 dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1229
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1230
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1231 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1232 # Add masked-javascripts tags to HTML file in the head and end
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1233 #===============================================================================
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1234
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1235 htmllines <- readLines(htmloutfile)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1236 htmllines[1] <- paste('<html>\n<head>\n', paste(prescripts, collapse='\n'), '\n</head>\n<body>')
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1237 cat(paste(htmllines, collapse='\n'), file = htmloutfile)
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1238 cat('\n', paste(postscripts, collapse='\n'), "\n",
dec87511835e planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1239 "</body>\n</html>\n", file = htmloutfile, append = TRUE);

Mercurial > repos > galaxyp > quantp

annotate quantp.r @ 3:9c70b9a95406 draft default tip