# HG changeset patch
# User yhoogstrate
# Date 1441287704 14400
# Node ID 6df940f979c8273267b34f70a9a110e3797f647c
# Parent ed809072dc950905601dbae71a0626061d883e71
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
diff -r ed809072dc95 -r 6df940f979c8 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml Tue Sep 01 08:05:27 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml Thu Sep 03 09:41:44 2015 -0400
@@ -15,6 +15,10 @@
source="both"
level="fatal"
description="Have the design- and expression-matrix been swapped?" />
+
@@ -30,7 +34,7 @@
description="LOCALE has not been set correctly" />
- echo $(R --version | grep version | grep -v GNU) ", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+ echo $(R --version | grep version | grep -v GNU)", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
R --vanilla --slave -f $R_script '--args
@@ -57,12 +61,24 @@
/dev/null
#end if
+ #if $output_MDSplot_logFC_coordinates:
+ $output_MDSplot_logFC_coordinates
+ #else:
+ /dev/null
+ #end if
+
#if $output_MDSplot_bcv:
$output_MDSplot_bcv
#else:
/dev/null
#end if
+ #if $output_MDSplot_bcv_coordinates:
+ $output_MDSplot_bcv_coordinates
+ #else:
+ /dev/null
+ #end if
+
#if $output_BCVplot:
$output_BCVplot
#else:
@@ -126,15 +142,20 @@
output_xpkm <- args[7] ##FPKM file - to be implemented
output_raw_counts <- args[8]
+
output_MDSplot_logFC <- args[9]
-output_MDSplot_bcv <- args[10]
-output_BCVplot <- args[11]
-output_MAplot <- args[12]
-output_PValue_distribution_plot <- args[13]
-output_hierarchical_clustering_plot <- args[14]
-output_heatmap_plot <- args[15]
-output_RData_obj <- args[16]
-output_format_images <- args[17]
+output_MDSplot_logFC_coordinates <- args[10]
+
+output_MDSplot_bcv <- args[11]
+output_MDSplot_bcv_coordinates <- args[12]
+
+output_BCVplot <- args[13]
+output_MAplot <- args[14]
+output_PValue_distribution_plot <- args[15]
+output_hierarchical_clustering_plot <- args[16]
+output_heatmap_plot <- args[17]
+output_RData_obj <- args[18]
+output_format_images <- args[19]
## Obtain read-counts
@@ -214,11 +235,16 @@
# hierarchical clustering makes use of the distance of the MDS
- if(output_MDSplot_logFC != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
+ if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
write("Calculating MDS plot (logFC method)",stdout())
- mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
+ n_dim <- nrow(dge\$samples)
+ mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
dev.off()# Kill it
+ # Reset to primary dimensions
+ mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1]
+ mds_distance_logFC\$y = mds_distance_logFC\$cmdscale.out[,2]
+
if(output_MDSplot_logFC != "/dev/null") {
write("Creating MDS plot (logFC method)",stdout())
if(output_format_images == "pdf") {
@@ -236,42 +262,60 @@
diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
- text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
+ text(mds_distance_logFC\$x,mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
rm(diff_x,diff_y)
dev.off()
- }
+ }
+
+ if(output_MDSplot_logFC_coordinates != "/dev/null") {
+ n_dim <- ncol(mds_distance_logFC\$cmdscale.out)
+ colnames(mds_distance_logFC\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
+ export <- data.frame(samples=rownames(mds_distance_logFC\$cmdscale.out),mds_distance_logFC\$cmdscale.out)
+ row.names(export) <- NULL
+ write.table(file=output_MDSplot_logFC_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
+ }
}
- if(output_MDSplot_bcv != "/dev/null") {
+ if(output_MDSplot_bcv != "/dev/null" || output_MDSplot_bcv_coordinates != "/dev/null" ) {
write("Creating MDS plot (bcv method)",stdout())
## 1. First create a virtual plot to obtain the desired coordinates
- pdf("bcvmds.pdf")
- mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))
- dev.off()# Kill it
+ n_dim <- nrow(dge\$samples)
+ mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
+ dev.off()
- ## 2. Re-plot the coordinates in a new figure with the size and settings.
- if(output_format_images == "pdf") {
- pdf(output_MDSplot_bcv,height=14,width=14)
- } else if(output_format_images == "svg") {
- svg(output_MDSplot_bcv,height=14,width=14)
- } else {
- ## png(output_MDSplot_bcv)
- ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+ if(output_MDSplot_logFC != "/dev/null") {
+ ## 2. Re-plot the coordinates in a new figure with the size and settings.
+ if(output_format_images == "pdf") {
+ pdf(output_MDSplot_bcv,height=14,width=14)
+ } else if(output_format_images == "svg") {
+ svg(output_MDSplot_bcv,height=14,width=14)
+ } else {
+ ## png(output_MDSplot_bcv)
+ ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+
+ bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3)
+ }
- bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3)
+ diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
+ diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
+ plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
+ points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
+ text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
+ rm(diff_x,diff_y)
+
+ dev.off()
}
- diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
- diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
- plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
- points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
- text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
- rm(diff_x,diff_y)
-
- dev.off()
+ if(output_MDSplot_bcv_coordinates != "/dev/null") {
+ n_dim <- ncol(mds_distance_BCV\$cmdscale.out)
+ colnames(mds_distance_BCV\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
+ export <- data.frame(samples=rownames(mds_distance_BCV\$cmdscale.out),mds_distance_BCV\$cmdscale.out)
+ row.names(export) <- NULL
+ write.table(file=output_MDSplot_bcv_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
+ }
}
@@ -423,7 +467,9 @@
-
+
+
+
@@ -457,6 +503,10 @@
+
+ outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)
+
+
outputs and ("make_output_MDSplot_bcv" in outputs)
@@ -467,6 +517,10 @@
+
+ outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)
+
+
outputs and ("make_output_BCVplot" in outputs)
diff -r ed809072dc95 -r 6df940f979c8 test-data/Differential_Gene_Expression/differentially_expressed_genes.tabular.txt
--- a/test-data/Differential_Gene_Expression/differentially_expressed_genes.tabular.txt Tue Sep 01 08:05:27 2015 -0400
+++ b/test-data/Differential_Gene_Expression/differentially_expressed_genes.tabular.txt Thu Sep 03 09:41:44 2015 -0400
@@ -1,29 +1,29 @@
"" "genes" "logFC" "logCPM" "LR" "PValue" "FDR"
-"15" "RET" 1.94897640107287 13.2940435307943 77.654599543179 1.22730171836821e-18 3.55917498326782e-17
-"24" "HSPA8" 0.607138087178611 18.9380827005326 16.8408380175314 4.06490891367457e-05 0.000589411792482813
-"12" "IFI44L" -0.665544707287885 11.7020333673755 13.7144720204488 0.000212808307971688 0.00205714697705965
-"10" "MYO18A" -0.608389235629078 14.1586814058554 10.0030349278008 0.00156282461000764 0.0113304784225554
-"4" "DDX11" 0.719283453206407 12.4597575302041 9.12036988131984 0.00252778847255745 0.0146611731408332
-"26" "NR2C2AP" 0.538719097450498 12.9331552590697 7.88314604327009 0.00498976028659176 0.0241171747185268
-"19" "RASSF3" -0.322613484306053 12.4964626371138 4.62652086564883 0.0314813398355935 0.130422693604602
-"3" "DDX17" -0.202898462175599 16.1804174471336 2.58563106106719 0.107837421983493 0.390910654690163
-"2" "USP26" -2.18026172235612 4.27316802151059 2.23964914988384 0.134511497925546 0.433425937760093
-"27" "INADL" -0.171517188407227 15.2186072712825 1.67097950802946 0.19612738879992 0.532259040389235
-"21" "LYSMD3" -0.195688416211883 13.32535006408 1.62863926869131 0.201891360147641 0.532259040389235
-"16" "IQCG" -0.204602031239979 10.1622224199572 1.27895197461613 0.258093988838365 0.623727139692716
-"14" "KCNAB3" 0.235558773538239 7.85434240586327 0.626910369343036 0.428490880664559 0.920477060517754
-"6" "SLC35D3" 0.732791849378157 4.62274850327991 0.571072605743573 0.449833005996972 0.920477060517754
-"20" "FUT8" -0.101052861033366 15.3006920075591 0.507763042822674 0.476108824405735 0.920477060517754
-"1" "COMMD10" 0.124183380838805 12.8850203875481 0.427219144496277 0.513356635936627 0.927280503730139
-"9" "TXLNB" -0.182677549934781 7.2825391341052 0.332700921323453 0.56407299924751 0.927280503730139
-"28" "TMEM31" -0.242966946412951 6.16897757110336 0.313478542290647 0.575553416108362 0.927280503730139
-"7" "GLOD4" -0.0680179216917625 13.8710260882794 0.180025725971987 0.671351132981887 0.998117639327786
-"17" "C20orf118" 0.14522927187254 6.73904801103973 0.160869778108134 0.688356992639853 0.998117639327786
-"22" "LMOD3" 0.0653797517936461 7.60390982671528 0.0485282387333417 0.825644327378613 1
-"8" "GIMAP7" 0.278076976843342 4.26623062002702 0.0410800206726094 0.839383539966141 1
-"23" "HIPK1" -0.00503549836369412 17.7957744498389 0.00154544013400937 0.968641570543933 1
-"13" "KHSRP" -0.00239769805103114 14.7206397592923 0.000263977505255752 0.987037033025321 1
-"11" "ATG4B" 0.00130641853526229 13.5252482941211 3.53338139831294e-05 0.995257222366413 1
+"15" "RET" 1.94897640107286 13.2940435307943 77.6545995415986 1.22730171935022e-18 3.55917498611563e-17
+"24" "HSPA8" 0.607138087178614 18.9380827005326 16.8408380186893 4.06490891119454e-05 0.000589411792123208
+"12" "IFI44L" -0.665544707287881 11.7020333673755 13.7144720195324 0.000212808308075529 0.00205714697806344
+"10" "MYO18A" -0.608389235629078 14.1586814058554 10.0030349277278 0.00156282461006963 0.0113304784230048
+"4" "DDX11" 0.719283453206409 12.4597575302041 9.1203698809081 0.00252778847312638 0.014661173144133
+"26" "NR2C2AP" 0.538719097450497 12.9331552590697 7.88314604309164 0.00498976028708414 0.0241171747209067
+"19" "RASSF3" -0.322613484306052 12.4964626371138 4.62652086549247 0.031481339838463 0.130422693616489
+"3" "DDX17" -0.202898462175601 16.1804174471336 2.58563106107022 0.107837421983287 0.390910654689415
+"2" "USP26" -2.18026172235612 4.27316802151059 2.23964990963176 0.134511431832489 0.433425724793576
+"27" "INADL" -0.171517188407228 15.2186072712825 1.67097950803399 0.196127388799313 0.532259040398981
+"21" "LYSMD3" -0.195688416211876 13.32535006408 1.62863926866461 0.201891360151338 0.532259040398981
+"16" "IQCG" -0.204602031239968 10.1622224199572 1.27895197435303 0.258093988887329 0.623727139811046
+"14" "KCNAB3" 0.235558773538239 7.85434240586327 0.626910368891663 0.42849088083079 0.920477060511131
+"6" "SLC35D3" 0.732791849378157 4.62274850327991 0.571073743098566 0.449832554709518 0.920477060511131
+"20" "FUT8" -0.10105286103336 15.3006920075591 0.507763042830561 0.476108824402309 0.920477060511131
+"1" "COMMD10" 0.124183380838807 12.8850203875481 0.427219144492929 0.513356635938278 0.927280503918676
+"9" "TXLNB" -0.182677549934781 7.2825391341052 0.332700920948795 0.564072999466928 0.927280503918676
+"28" "TMEM31" -0.242966946412956 6.16897757110336 0.313478542098543 0.575553416225385 0.927280503918676
+"7" "GLOD4" -0.0680179216917574 13.8710260882794 0.180025725971447 0.671351132982351 0.998117639846733
+"17" "C20orf118" 0.14522927187254 6.73904801103973 0.16086977771818 0.688356992997747 0.998117639846733
+"22" "LMOD3" 0.065379751793664 7.60390982671528 0.0485282385969317 0.825644327619727 1
+"8" "GIMAP7" 0.278076976843342 4.26623062002702 0.0410821671265458 0.839379401017925 1
+"23" "HIPK1" -0.0050354983636938 17.7957744498389 0.00154544012787028 0.968641570606185 1
+"13" "KHSRP" -0.00239769805103114 14.7206397592923 0.000263977502370949 0.987037033096146 1
+"11" "ATG4B" 0.00130641853526229 13.5252482941211 3.5333815787908e-05 0.995257222245289 1
"5" "PTPN20B" 0 4.09631395702755 0 1 1
"18" "GPIHBP1" 0 4.09631395702755 0 1 1
"25" "TAS2R39" 0 4.09631395702755 0 1 1