# 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?" />
+        <regex match="Error in eval\(expr, envir, enclos\)"
+               source="both"
+               level="fatal"
+               description="You have most likely used a condition in the contrast, that is not present in the Design matrix" />
         <regex match="Execution halted"
                source="both"
                level="fatal" />
@@ -30,7 +34,7 @@
                description="LOCALE has not been set correctly" />
     </stdio>
     
-    <version_command>echo $(R --version | grep version | grep -v GNU) ", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
+    <version_command>echo $(R --version | grep version | grep -v GNU)", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
     
     <command>
         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 @@
         <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes">
             <option value="make_output_raw_counts">Raw counts table</option>
             <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option>
-            <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; much slower)</option>
+            <option value="make_output_MDSplot_logFC_coordinates">MDS-plot coordinates table (logFC-method)</option>
+            <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; slow)</option>
+            <option value="make_output_MDSplot_bcv_coordinates">MDS-plot coordinates table (BCV-method; slow)</option>
             <option value="make_output_BCVplot">BCV-plot</option>
             <option value="make_output_MAplot">MA-plot</option>
             <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
@@ -457,6 +503,10 @@
             </change_format>
         </data>
         
+        <data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (logFC method)">
+            <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter>
+        </data>
+        
         <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)">
             <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter>
             
@@ -467,6 +517,10 @@
             </change_format>
         </data>
         
+        <data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (BCV method)">
+            <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter>
+        </data>
+        
         <data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
             <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
             
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