quantp: quantp.r annotate

annotate quantp.r @ 0:f1db758949f4 draft

planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6

author	galaxyp
date	Fri, 14 Sep 2018 12:22:13 -0400
parents
children	dec87511835e

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$Group = tempgrp;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	16 png(outfile, width = 6, height = 6, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	17 # bitmap(outfile, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	18 g = autoplot(prcomp(select(tempdf, -Group)), data = tempdf, colour = 'Group', size=3);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	19 plot(g);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	20 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	21 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	22
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	23 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	24 # Regression and Cook's distance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	25 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	26 singlesample_regression = function(PE_TE_data,htmloutfile, append=TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	27 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	28 rownames(PE_TE_data) = PE_TE_data$PE_ID;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	29 regmodel = lm(PE_abundance~TE_abundance, data=PE_TE_data);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	30 regmodel_summary = summary(regmodel);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	31
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	32 cat("<font><h3>Linear Regression model fit between Proteome and Transcriptome data</h3></font>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	33 "<p>Assuming a linear relationship between Proteome and Transcriptome data, we here fit a linear regression model.</p>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	34 '<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	35 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	36
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	37 cat("<tr><td>Formula</td><td>","PE_abundance~TE_abundance","</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	38 "<tr><td colspan='2' align='center'> <b>Coefficients</b></td>","</tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	39 "<tr><td>",names(regmodel$coefficients[1]),"</td><td>",regmodel$coefficients[1]," (Pvalue:", regmodel_summary$coefficients[1,4],")","</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	40 "<tr><td>",names(regmodel$coefficients[2]),"</td><td>",regmodel$coefficients[2]," (Pvalue:", regmodel_summary$coefficients[2,4],")","</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	41 "<tr><td colspan='2' align='center'> <b>Model parameters</b></td>","</tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	42 "<tr><td>Residual standard error</td><td>",regmodel_summary$sigma," (",regmodel_summary$df[2]," degree of freedom)</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	43 "<tr><td>F-statistic</td><td>",regmodel_summary$fstatistic[1]," ( on ",regmodel_summary$fstatistic[2]," and ",regmodel_summary$fstatistic[3]," degree of freedom)</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	44 "<tr><td>R-squared</td><td>",regmodel_summary$r.squared,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	45 "<tr><td>Adjusted R-squared</td><td>",regmodel_summary$adj.r.squared,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	46 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	47
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	48 cat("</table>\n", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	49
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	50 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	51 "<font color='#ff0000'><h3>Regression and diagnostics plots</h3></font>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	52 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	53
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	54 outplot = paste(outdir,"/PE_TE_lm_1.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	55 png(outplot, width = 10, height = 10, units = 'in',res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	56 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	57 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	58 plot(regmodel, 1, cex.lab=1.5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	59 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	60
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	61 outplot = paste(outdir,"/PE_TE_lm_2.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	62 png(outplot,width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	63 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	64 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	65 plot(regmodel, 2, cex.lab=1.5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	66 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	67
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	68 outplot = paste(outdir,"/PE_TE_lm_5.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));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	72 plot(regmodel, 5, cex.lab=1.5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	73 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	74
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	75 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	76
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	77 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	78 '<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	79 '<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	80 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	81
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	82 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	83 '<tr><td align=center><img src="PE_TE_lm_1.png" width=600 height=600></td><td align=center><img src="PE_TE_lm_2.png" width=600 height=600></td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	84 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	85
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	86 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	87 '<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	88 '<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	89 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	90
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	91
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	92 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	93 # Residuals data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	94 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	95 res_all = regmodel$residuals;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	96 res_mean = mean(res_all);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	97 res_sd = sd(res_all);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	98 res_diff = (res_all-res_mean);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	99 res_zscore = res_diff/res_sd;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	100 # res_outliers = res_all[which((res_zscore > 2)\|(res_zscore < -2))]
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	101
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	102
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	103 tempind = which((res_zscore > 2)\|(res_zscore < -2));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	104 res_PE_TE_data_no_outlier = PE_TE_data[-tempind,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	105 res_PE_TE_data_no_outlier$residuals = res_all[-tempind];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	106 res_PE_TE_data_outlier = PE_TE_data[tempind,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	107 res_PE_TE_data_outlier$residuals = res_all[tempind];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	108
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	109 # Save the complete table for download (influential_observations)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	110 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)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	111 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	112 outdatafile = paste(outdir,"/PE_TE_outliers_residuals.txt", sep="", collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	113 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	114
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	115
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	116 # Save the complete table for download (non influential_observations)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	117 temp_all_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, res_all)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	118 colnames(temp_all_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	119 outdatafile = paste(outdir,"/PE_TE_abundance_residuals.txt", sep="", collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	120 write.table(temp_all_data, file=outdatafile, row.names=F, sep="\t", quote=F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	121
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	122
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	123 cat('<br><h2 id="inf_obs"><font color=#ff0000>Outliers based on the residuals from regression analysis</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	124 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	125 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	126 '<tr bgcolor="#7a0019"><th colspan=2><font color=#ffcc33>Residuals from Regression</font></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	127 '<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	128 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	129
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	130 cat("<tr><td>Mean Residual value</td><td>",res_mean,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	131 "<tr><td>Standard deviation (Residuals)</td><td>",res_sd,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	132 '<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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	133 '<tr><td colspan=2 align=center><font size=4>(<b><a href=PE_TE_abundance_residuals.txt target="_blank">Download the complete residuals data here</a></b>)</font></td></td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	134 "</table><br><br>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	135 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	136
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	137 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	138
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	139
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	140 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	141
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	142 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	143 '<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	144 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	145
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	146 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	147 '<tr><td align=center><img src="PE_TE_lm_5.png" width=600 height=600></td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	148 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	149
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	150 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	151 '<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	152 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	153
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	154
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	155
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	156 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	157 # Cook's Distance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	158 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	159 cat('<hr/><h2 id="inf_obs"><font color=#ff0000>INFLUENTIAL OBSERVATIONS</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	160 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	161 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	162 '<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	163 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	164
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	165 cooksd <- cooks.distance(regmodel);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	166
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	167 outplot = paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	168 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	169 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	170 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	171 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	172 sel_outlier=which(cooksd>=as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	173 sel_nonoutlier=which(cooksd<as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	174 points(sel_outlier, cooksd[sel_outlier],pch="*", cex=2, cex.lab=1.5, col="red")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	175 points(sel_nonoutlier, cooksd[sel_nonoutlier],pch="*", cex=2, cex.lab=1.5, col="black")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	176 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	177 #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	178 dev.off();
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 '<img src="PE_TE_lm_cooksd.png" width=800 height=800>',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	182 '<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	183 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	184
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	185 tempind = which(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	186 PE_TE_data_no_outlier = PE_TE_data[-tempind,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	187 PE_TE_data_no_outlier$cooksd = cooksd[-tempind];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	188 PE_TE_data_outlier = PE_TE_data[tempind,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	189 PE_TE_data_outlier$cooksd = cooksd[tempind];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	190 a = sort(PE_TE_data_outlier$cooksd, decreasing=T, index.return=T);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	191 PE_TE_data_outlier_sorted = PE_TE_data_outlier[a$ix,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	192
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	193 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	194 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	195 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	196
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	197 # Save the complete table for download (influential_observations)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	198 temp_outlier_data = data.frame(PE_TE_data_outlier$PE_ID, PE_TE_data_outlier$TE_abundance, PE_TE_data_outlier$PE_abundance, PE_TE_data_outlier$cooksd)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	199 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	200 outdatafile = paste(outdir,"/PE_TE_influential_observation.txt", sep="", collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	201 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	202
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	203
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	204 # Save the complete table for download (non influential_observations)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	205 temp_no_outlier_data = data.frame(PE_TE_data_no_outlier$PE_ID, PE_TE_data_no_outlier$TE_abundance, PE_TE_data_no_outlier$PE_abundance, PE_TE_data_no_outlier$cooksd)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	206 colnames(temp_no_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	207 outdatafile = paste(outdir,"/PE_TE_non_influential_observation.txt", sep="", collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	208 write.table(temp_no_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	209
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	210
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	211 cat("<tr><td>Mean Cook\'s distance</td><td>",mean(cooksd, na.rm=T),"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	212 "<tr><td>Total influential observations (Cook\'s distance > ",cookdist_upper_cutoff," * mean Cook\'s distance)</td><td>",length(tempind),"</td>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	213
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	214 "<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",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	215 "</table><br><br>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	216 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	217
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	218
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	219 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	220 # Scatter plot after removal of influential points
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	221 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	222 outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	223 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	224 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	225 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	226 # bitmap(outplot,"png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	227 g = ggplot(PE_TE_data_no_outlier, aes(x=TE_abundance, y=PE_abundance))+geom_point() + geom_smooth() + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + xlim(min_lim,max_lim) + ylim(min_lim,max_lim);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	228 suppressMessages(plot(g));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	229 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	230
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	231 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);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	232 # Before
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	233 cat("<tr><td align=center><!--<font color='#ff0000'><h3>Scatter plot between Proteome and Transcriptome Abundance</h3></font>\n-->", '<img src="TE_PE_scatter.png" width=600 height=600></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	234
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	235 # After
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	236 cat("<td align=center>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	237 '<img src="AbundancePlot_scatter_without_outliers.png" width=600 height=600></td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	238 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	239 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	240
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	241
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	242 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	243 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	244 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	245
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	246 cat('<tr><td>\n', file = htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	247 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	248 cat('</td>\n', file = htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	249
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	250
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	251 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	252 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	253
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	254 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	255 "<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	256 "<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	257 file = htmloutfile, append = TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	258 cat("</table></td></tr></table>\n", file = htmloutfile, append = TRUE)
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
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	262 if(dim(PE_TE_data_outlier)[1]<10)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	263 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	264 tab_n_row = dim(PE_TE_data_outlier)[1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	265 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	266 tab_n_row = 10;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	267 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	268
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	269 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>    ",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	270 "<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",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	271 '<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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	272 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	273
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	274 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	275 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",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	276 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	277
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	278
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	279 for(i in 1:tab_n_row)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	280 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	281 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	282 '<tr>','<td>',as.character(PE_TE_data_outlier_sorted[i,1]),'</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	283 '<td>',format(PE_TE_data_outlier_sorted[i,2], scientific=F),'</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	284 '<td>',PE_TE_data_outlier_sorted[i,4],'</td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	285 '<td>',format(PE_TE_data_outlier_sorted[i,5], scientific=F),'</td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	286 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	287 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	288 cat('</table><br><br>\n',file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	289
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	290
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	291 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	292
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	293
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	294
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	295 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	296 # Heatmap
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	297 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	298 singlesample_heatmap=function(PE_TE_data, htmloutfile, hm_nclust){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	299 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	300 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	301
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	302 hc=hclust(dist(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")])))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	303 hm_cluster = cutree(hc,k=hm_nclust);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	304
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	305 outplot = paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	306 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	307 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	308 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	309 hmap = heatmap.2(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]), trace="none", cexCol=1, col=greenred(100),Colv=F, labCol=c("Proteins","Transcripts"), scale="col", hclustfun = hclust, distfun = dist);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	310 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	311
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	312 cat('<tr><td align=center colspan="2"><img src="PE_TE_heatmap.png" width=800 height=800></td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	313 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	314
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	315
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	316 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	317 colnames(temp_PE_TE_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cluster (Hierarchical clustering)")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	318 tempoutfile = paste(outdir,"/PE_TE_hc_clusterpoints.txt",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	319 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	320
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	321
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	322 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	323 file = htmloutfile, append = TRUE);
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
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	327 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	328 # K-means clustering
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	329 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	330 singlesample_kmeans=function(PE_TE_data, htmloutfile, nclust){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	331 PE_TE_data_kdata = PE_TE_data;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	332 k1 = kmeans(PE_TE_data_kdata[,c("PE_abundance","TE_abundance")], nclust);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	333 outplot = paste(outdir,"/PE_TE_kmeans.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	334 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	335 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	336 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	337 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	338 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	339 legend(1, 95, legend="Cluster 2", col="green", lty=1:1, cex=0.8)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	340
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	341
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	342 ind=which(k1$cluster==1);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	343 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="red", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	344 ind=which(k1$cluster==2);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	345 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	346 ind=which(k1$cluster==3);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	347 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="blue", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	348 ind=which(k1$cluster==4);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	349 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	350 ind=which(k1$cluster==5);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	351 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="black", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	352 ind=which(k1$cluster==6);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	353 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	354 ind=which(k1$cluster==7);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	355 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="gold", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	356 ind=which(k1$cluster==8);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	357 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	358 ind=which(k1$cluster==9);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	359 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="yellow", pch=16);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	360 ind=which(k1$cluster==10);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	361 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	362 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	363
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	364 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	365 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	366
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	367 tempind = order(k1$cluster);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	368 tempoutfile = paste(outdir,"/PE_TE_kmeans_clusterpoints.txt",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	369 write.table(data.frame(PE_TE_data_kdata[tempind, ], Cluster=k1$cluster[tempind]), file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	370
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	371
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	372 cat('<tr><td colspan="2" align=center><img src="PE_TE_kmeans.png" width=800 height=800></td></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	373 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	374 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	375 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	376
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	377 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	378
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	379 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	380 # scatter plot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	381 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	382 singlesample_scatter = function(PE_TE_data, outfile)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	383 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	384 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	385 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	386 png(outfile, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	387 # bitmap(outfile, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	388 g = ggplot(PE_TE_data, aes(x=TE_abundance, y=PE_abundance))+geom_point() + geom_smooth() + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + xlim(min_lim,max_lim) + ylim(min_lim,max_lim);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	389 suppressMessages(plot(g));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	390 # plot(g);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	391 dev.off();
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 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	395 # Correlation table
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	396 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	397 singlesample_cor = function(PE_TE_data, htmloutfile, append=TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	398 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	399 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	400 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	401 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	402
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	403 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	404 '<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	405 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	406
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	407 cat(
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	408 "<tr><td>Correlation method</td><td>",cor_result_pearson$method,"</td><td>",cor_result_spearman$method,"</td><td>",cor_result_kendall$method,"</td></tr>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	409 "<tr><td>Correlation coefficient</td><td>",cor_result_pearson$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	410 file = htmloutfile, append = TRUE)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	411 cat("</table>\n", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	412
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	413 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	414
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	415 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	416 # Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	417 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	418 multisample_boxplot = function(df, sampleinfo_df, outfile, fill_leg, user_xlab, user_ylab)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	419 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	420 tempdf = df[,-1, drop=FALSE];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	421 tempdf = t(tempdf) %>% as.data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	422 tempdf[is.na(tempdf)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	423 tempdf$Sample = rownames(tempdf);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	424 tempdf1 = melt(tempdf, id.vars = "Sample");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	425 tempdf1$Group = sampleinfo_df[tempdf1$Sample,2];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	426 png(outplot, width = 6, height = 6, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	427 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	428 if(fill_leg=="Yes")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	429 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	430 g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + geom_boxplot() + labs(x=user_xlab) + labs(y=user_ylab)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	431 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	432 if(fill_leg=="No")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	433 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	434 tempdf1$Group = c("case", "control")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	435 g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + geom_boxplot() + labs(x=user_xlab) + labs(y=user_ylab)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	436 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	437 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	438 plot(g);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	439 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	440 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	441
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	442
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	443 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	444 # Mean or Median of Replicates
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	445 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	446
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	447 mergeReplicates = function(TE_df,PE_df, sampleinfo_df, method)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	448 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	449 grps = unique(sampleinfo_df[,2]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	450
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	451 TE_df_merged <<- sapply(grps, function(x){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	452 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	453 if(length(tempsample)!=1){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	454 apply(TE_df[,tempsample],1,method);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	455 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	456 return(TE_df[,tempsample]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	457 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	458 });
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	459 TE_df_merged <<- data.frame(as.character(TE_df[,1]), TE_df_merged);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	460 colnames(TE_df_merged) = c(colnames(TE_df)[1], grps);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	461
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	462 PE_df_merged <<- sapply(grps, function(x){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	463 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	464 if(length(tempsample)!=1){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	465 apply(PE_df[,tempsample],1,method);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	466 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	467 return(PE_df[,tempsample]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	468 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	469 });
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	470
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	471 PE_df_merged <<- data.frame(as.character(PE_df[,1]), PE_df_merged);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	472 colnames(PE_df_merged) = c(colnames(PE_df)[1], grps);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	473
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	474 #sampleinfo_df_merged = data.frame(Sample = grps, Group = grps, stringsAsFactors = F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	475 sampleinfo_df_merged = data.frame(Sample = grps, Group = "Group", stringsAsFactors = F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	476
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	477 return(list(TE_df_merged = TE_df_merged, PE_df_merged = PE_df_merged, sampleinfo_df_merged = sampleinfo_df_merged));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	478 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	479
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	480 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	481 # (T-Test or Wilcoxon ranksum test) and Volcano Plot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	482 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	483
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	484 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	485 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	486
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	487 PE_colnames = colnames(PE_df_data);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	488 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	489 control_ind <<- sapply(control_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	490 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	491 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	492
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	493 if(method=="mean"){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	494 #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])$p.value);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	495 PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	496 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	497 if(method=="median"){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	498 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$p.value)}})
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	499 # PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	500 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	501 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	502 PE_adj_pval = p.adjust(PE_pval, method = correction_method, n = length(PE_pval))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	503
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	504
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	505 TE_colnames = colnames(TE_df_data);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	506 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	507 control_ind <<- sapply(control_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	508 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	509 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	510
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	511 if(method=="mean"){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	512 # 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])$p.value);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	513 TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	514 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	515 if(method=="median"){
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	516 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$p.value)}})
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	517 # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	518 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	519 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	520 TE_adj_pval = p.adjust(TE_pval, method = correction_method, n = length(TE_pval))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	521
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	522
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	523 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);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	524 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)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	525 outdatafile = paste(outdir,"/PE_TE_logfold_pval.txt", sep="", collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	526 write.table(PE_TE_logfold_pval, file=outdatafile, row.names=F, sep="\t", quote=F);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	527 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",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	528 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	529
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	530 if(length(condition_ind)!=1)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	531 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	532 # Volcano Plot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	533
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	534 if(volc_with=="adj_pval")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	535 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	536 PE_pval = PE_adj_pval
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	537 TE_pval = TE_adj_pval
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	538 volc_ylab = "-log10 Adjusted p-value";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	539 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	540 if(volc_with=="pval")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	541 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	542 volc_ylab = "-log10 p-value";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	543 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	544 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	545 outplot = paste(outdir,"/PE_volcano.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	546 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	547 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	548 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	549
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	550 plot(PE_df_logfold$LogFold, -log10(PE_pval),
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	551 xlab="log2 fold change", ylab=volc_ylab,
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	552 type="n")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	553 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
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	554 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="black")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	555 #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
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	556 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	557 sel1 <- which(PE_pval<=0.05)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	558 sel=intersect(sel,sel1)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	559 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="red")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	560 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	561 sel1 <- which(PE_pval>0.05)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	562 sel=intersect(sel,sel1)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	563 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="blue")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	564 abline(h = -log(0.05,base=10), col="red", lty=2)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	565 abline(v = log(2,base=2), col="red", lty=2)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	566 abline(v = log(0.5,base=2), col="red", lty=2)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	567 dev.off();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	568
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	569
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	570
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	571 outplot = paste(outdir,"/TE_volcano.png",sep="",collapse="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	572 png(outplot, width = 10, height = 10, units = 'in', res=300);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	573 # bitmap(outplot, "png16m");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	574 par(mfrow=c(1,1));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	575
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	576 plot(TE_df_logfold$LogFold, -log10(TE_pval),
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	577 xlab="log2 fold change", ylab=volc_ylab,
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	578 type="n")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	579 sel <- which((TE_df_logfold$LogFold<=log(2,base=2))&(TE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	580 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="black")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	581 #sel <- which((TE_df_logfold$LogFold>log(2,base=2))&(TE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	582 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	583 sel1 <- which(TE_pval<=0.05)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	584 sel=intersect(sel,sel1)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	585 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="red")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	586 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	587 sel1 <- which(TE_pval>0.05)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	588 sel=intersect(sel,sel1)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	589 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="blue")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	590 abline(h = -log(0.05,base=10), col="red", lty=2)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	591 abline(v = log(2,base=2), col="red", lty=2)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	592 abline(v = log(0.5,base=2), col="red", lty=2)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	593 dev.off();
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
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	597 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);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	598 cat("<tr><td align=center>", '<img src="TE_volcano.png" width=600 height=600></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	599 cat("<td align=center>",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	600 '<img src="PE_volcano.png" width=600 height=600></td></tr></table><br>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	601 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	602 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	603 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>',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	604 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	605 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	606
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	607 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	608
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	609
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	610 #***************************************************************************************************************************************
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	611 # Functions: End
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	612 #***************************************************************************************************************************************
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	613
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	614
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	615
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	616
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	617 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	618 # Arguments
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	619 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	620 noargs = 12;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	621 args = commandArgs(trailingOnly = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	622 if(length(args) != noargs)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	623 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	624 stop(paste("Please check usage. Number of arguments is not equal to ",noargs,sep="",collapse=""));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	625 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	626
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	627 mode = args[1]; # "multiple" or "logfold"
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	628 method = args[2]; # "mean" or "median"
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	629 sampleinfo_file = args[3];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	630 proteome_file = args[4];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	631 transcriptome_file = args[5];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	632 correction_method = args[6];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	633 cookdist_upper_cutoff = args[7];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	634 numCluster = args[8];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	635 hm_nclust = args[9];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	636 volc_with = args[10];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	637
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	638 htmloutfile = args[11]; # html output file
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	639 outdir = args[12]; # html supporting files
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	640
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	641
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	642 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	643 # Check for file existance
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	644 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	645 if(! file.exists(proteome_file))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	646 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	647 stop(paste("Proteome Data file does not exists. Path given: ",proteome_file,sep="",collapse=""));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	648 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	649 if(! file.exists(transcriptome_file))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	650 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	651 stop(paste("Transcriptome Data file does not exists. Path given: ",transcriptome_file,sep="",collapse=""));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	652 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	653
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	654 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	655 # Load library
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	656 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	657 options(warn=-1);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	658
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	659 suppressPackageStartupMessages(library(dplyr));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	660 suppressPackageStartupMessages(library(data.table));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	661 suppressPackageStartupMessages(library(gplots));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	662 suppressPackageStartupMessages(library(ggplot2));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	663 suppressPackageStartupMessages(library(ggfortify));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	664
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	665 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	666 # Select mode and parse experiment design file
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	667 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	668 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	669 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	670 expDesign = fread(sampleinfo_file, header = FALSE, stringsAsFactors = FALSE, sep="\t") %>% data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	671 expDesign_cc = expDesign[1:2,];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	672
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	673 sampleinfo_df = expDesign[3:nrow(expDesign),];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	674 rownames(sampleinfo_df)=1:nrow(sampleinfo_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	675 colnames(sampleinfo_df) = c("Sample","Group");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	676
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	677 condition_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	678 condition_g_name = "case";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	679 control_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	680 control_g_name = "control";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	681 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),2] = "case";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	682 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),2] = "control";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	683 sampleinfo_df_orig = sampleinfo_df;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	684 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	685
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	686 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	687 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	688 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	689 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	690
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	691 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	692 # Parse Transcriptome data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	693 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	694 TE_df_orig = fread(transcriptome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	695 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	696 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	697 TE_df = TE_df_orig[,c(colnames(TE_df_orig)[1],condition_cols,control_cols)];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	698 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	699 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	700 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	701 TE_df = TE_df_orig;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	702 colnames(TE_df) = c("Genes", "LogFold");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	703 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	704 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	705 # Parse Proteome data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	706 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	707 PE_df_orig = fread(proteome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	708 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	709 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	710 PE_df = PE_df_orig[,c(colnames(PE_df_orig)[1],condition_cols,control_cols)];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	711 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	712 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	713 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	714 PE_df = PE_df_orig;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	715 colnames(PE_df) = c("Genes", "LogFold");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	716 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	717
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	718 #=============================================================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	719 # Create directory structures and then set the working directory to output directory
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	720 #=============================================================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	721 if(! file.exists(outdir))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	722 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	723 dir.create(outdir);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	724 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	725 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	726 # Write initial data summary in html outfile
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	727 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	728 cat("<html><head></head><body>\n", file = htmloutfile);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	729
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	730 cat("<h1><u>QuanTP: Association between abundance ratios of transcript and protein</u></h1><hr/>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	731 "<font><h3>Input data summary</h3></font>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	732 "<ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	733 "<li>Abbreviations used: PE (Proteome data) and TE (Transcriptome data)","</li><br>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	734 "<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	735 "<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	736 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	737
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	738 cat("<h3 id=table_of_content>Table of Contents:</h3>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	739 "<ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	740 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	741 "<li><a href=#corr_data>Correlation</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	742 "<li><a href=#regression_data>Regression analysis</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	743 "<li><a href=#inf_obs>Influential observations</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	744 "<li><a href=#cluster_data>Cluster analysis</a></li></ul><hr/>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	745 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	746 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	747 # Find common samples
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	748 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	749 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	750
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	751 if(length(common_samples)==0)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	752 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	753 stop("No common samples found ");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	754 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	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 # Create subsets based on common samples
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	759 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	760 TE_df = select(TE_df, 1, common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	761 PE_df = select(PE_df, 1, common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	762 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	763 rownames(sampleinfo_df) = sampleinfo_df[,1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	764
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	765 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	766 # Check for number of rows similarity
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	767 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	768 if(nrow(TE_df) != nrow(PE_df))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	769 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	770 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	771 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	772 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	773
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	774 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	775 # Number of groups
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	776 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	777 ngrps = unique(sampleinfo_df[,2]) %>% length();
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	778 grps = unique(sampleinfo_df[,2]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	779 names(grps) = grps;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	780
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	781 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	782 # Change column1 name
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	783 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	784 colnames(TE_df)[1] = "Gene";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	785 colnames(PE_df)[1] = "Protein";
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	786
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	787 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	788 # Treat missing values
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	789 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	790 TE_nacount = sum(is.na(TE_df));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	791 PE_nacount = sum(is.na(PE_df));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	792
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	793 TE_df[is.na(TE_df)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	794 PE_df[is.na(PE_df)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	795
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 # Decide based on analysis mode
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	799 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	800 if(mode=="logfold")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	801 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	802 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	803 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	804
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	805 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	806 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	807 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	808 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	809 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	810 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	811
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	812 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	813 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	814 cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	815 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance data");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	816
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	817 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	818 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	819
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	820 # TE PE scatter
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	821 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	822 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);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	823 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800></td></tr>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	824 PE_TE_data = data.frame(PE_df, TE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	825 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	826 singlesample_scatter(PE_TE_data, outplot);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	827
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	828 # TE PE Cor
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	829 cat("<tr><td align=center>", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	830 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	831 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	832 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	833 cat('</td></table>',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	834 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	835
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	836 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	837 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	838
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	839 # TE PE Regression
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	840 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	841
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	842 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	843 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	844
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	845 # TE PE Heatmap
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	846 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	847
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	848
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	849 # TE PE Clustering (kmeans)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	850 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	851
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	852 }else{
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	853 if(mode=="multiple")
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	854 {
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	855 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	856 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	857
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	858 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	859 outplot = paste(outdir,"/Box_TE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	860 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	861 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	862 "<tr><td align=center>", '<img src="Box_TE_all_rep.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	863 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	864 colnames(temp_df_te_data) = colnames(TE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	865 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance (log)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	866
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	867 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	868 outplot = paste(outdir,"/Box_PE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	869 cat("<td align=center>", '<img src="Box_PE_all_rep.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	870 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	871 colnames(temp_df_pe_data) = colnames(PE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	872 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance (log)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	873
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	874 # Calc TE PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	875 outplot = paste(outdir,"/PCA_TE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	876 multisample_PCA(TE_df, sampleinfo_df, outplot);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	877
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	878 # Calc PE PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	879 outplot = paste(outdir,"/PCA_PE_all_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	880 multisample_PCA(PE_df, sampleinfo_df, outplot);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	881
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	882
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	883 # Replicate mode
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	884 templist = mergeReplicates(TE_df,PE_df, sampleinfo_df, method);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	885 TE_df = templist$TE_df_merged;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	886 PE_df = templist$PE_df_merged;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	887 sampleinfo_df = templist$sampleinfo_df_merged;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	888 rownames(sampleinfo_df) = sampleinfo_df[,1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	889
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	890 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	891 outplot = paste(outdir,"/Box_TE_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	892 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	893 "<tr><td align=center>", '<img src="Box_TE_rep.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	894 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	895 colnames(temp_df_te_data) = colnames(TE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	896 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Transcript Abundance (log)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	897
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	898 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	899 outplot = paste(outdir,"/Box_PE_rep.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	900 cat("<td align=center>", '<img src="Box_PE_rep.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	901 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	902 colnames(temp_df_pe_data) = colnames(PE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	903 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Protein Abundance (log)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	904
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	905 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	906 # Calculating log fold change and running the "single" code part
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	907 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	908
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	909 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	910 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)));
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	911
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	912 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	913 # Treat missing values
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	914 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	915
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	916 TE_df[is.infinite(TE_df[,2]),2] = NA;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	917 PE_df[is.infinite(PE_df[,2]),2] = NA;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	918 TE_df[is.na(TE_df)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	919 PE_df[is.na(PE_df)] = 0;
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	920
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	921 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	922 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	923 # Find common samples
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	924 #===============================================================================
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	925
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	926 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	927 TE_df = select(TE_df, 1, common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	928 PE_df = select(PE_df, 1, common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	929 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	930 rownames(sampleinfo_df) = sampleinfo_df[,1];
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	931
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	932 # TE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	933 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	934 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	935 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	936 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	937 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Transcript Abundance fold-change (log2)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	938
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	939 # PE Boxplot
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	940 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	941 cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	942 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Protein Abundance fold-change(log2)");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	943
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	944
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	945 # Log Fold Data
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	946 perform_Test_Volcano(TE_df_orig,PE_df_orig,TE_df, PE_df,sampleinfo_df_orig,method,correction_method,volc_with)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	947
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	948
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	949
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	950 # Print PCA
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	951
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	952 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	953 "<tr><td align=center>", '<img src="PCA_TE_all_rep.png" width=500 height=500></td>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	954 "<td align=center>", '<img src="PCA_PE_all_rep.png" width=500 height=500></td></tr></table>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	955 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	956
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	957
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	958
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	959 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	960 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	961
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	962 # TE PE scatter
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	963 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	964 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	965 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800></td>\n', file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	966 PE_TE_data = data.frame(PE_df, TE_df);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	967 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	968 singlesample_scatter(PE_TE_data, outplot);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	969
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	970 # TE PE Cor
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	971 cat("<tr><td align=center>\n", file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	972 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	973 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',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	974 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	975 cat('</td></table>',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	976 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	977
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	978 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	979 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	980
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	981 # TE PE Regression
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	982 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	983
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	984 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	985 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	986
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	987 #TE PE Heatmap
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	988 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	989
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	990 #TE PE Clustering (kmeans)
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	991 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	992
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	993 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	994 }
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	995 cat("<h3>Go To:</h3>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	996 "<ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	997 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	998 "<li><a href=#corr_data>Correlation</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	999 "<li><a href=#regression_data>Regression analysis</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1000 "<li><a href=#inf_obs>Influential observations</a></li>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1001 "<li><a href=#cluster_data>Cluster analysis</a></li></ul>\n",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1002 "<br><a href=#>TOP</a>",
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1003 file = htmloutfile, append = TRUE);
f1db758949f4 planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1004 cat("</body></html>\n", file = htmloutfile, append = TRUE);

Mercurial > repos > galaxyp > quantp

annotate quantp.r @ 0:f1db758949f4 draft