# HG changeset patch
# User proteore
# Date 1536760895 14400
# Node ID 5569a3f066cf95aca37e72055299210247a33d06
# Parent  92dfcfb03adde9ab7376fa59eec1510633d24beb
planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty

diff -r 92dfcfb03add -r 5569a3f066cf enrichment_v3.R
--- a/enrichment_v3.R	Wed Aug 22 10:39:30 2018 -0400
+++ b/enrichment_v3.R	Wed Sep 12 10:01:35 2018 -0400
@@ -250,11 +250,8 @@
 	count = data$Significant
   
 	labely = paste("GO terms",onto,sep=" ")
-	png(filename="dotplot.png",res=300, width = 3200, height = 3200, units = "px")
-	sp1 = ggplot(data,aes(x=geneRatio,y=goTerms, color=values,size=count)) +geom_point() + scale_colour_gradientn(colours=c("red","violet","blue")) + xlab("Gene Ratio") + ylab(labely) + labs(color="p-values\n") 
-
-	plot(sp1)
-	dev.off()
+	ggplot(data,aes(x=geneRatio,y=goTerms, color=values,size=count)) +geom_point( ) + scale_colour_gradientn(colours=c("red","violet","blue")) + xlab("Gene Ratio") + ylab(labely) + labs(color="p-values\n" ) 
+  ggsave("dotplot.png", device = "png", dpi = 320, limitsize = TRUE, width = 15, height = 15, units="cm")
 }
 
 createBarPlot = function(data, onto){
@@ -266,12 +263,10 @@
   values = as.numeric(values)
   goTerms = data$Term
 	count = data$Significant
-	png(filename="barplot.png",res=300, width = 3200, height = 3200, units = "px")
 	
 	labely = paste("GO terms",onto,sep=" ")
-  p<-ggplot(data, aes(x=goTerms, y=count,fill=values)) + ylab("Gene count") + xlab(labely) +geom_bar(stat="identity") + scale_fill_gradientn(colours=c("red","violet","blue")) + coord_flip() + labs(fill="p-values\n") 
-	plot(p)
-	dev.off()
+  ggplot(data, aes(x=goTerms, y=count,fill=values,scale(scale = 0.5))) + ylab("Gene count") + xlab(labely) +geom_bar(stat="identity") + scale_fill_gradientn(colours=c("red","violet","blue")) + coord_flip() + labs(fill="p-values\n") 
+  ggsave("barplot.png", device = "png", dpi = 320, limitsize = TRUE, width = 15, height = 15, units="cm")
 }
 
 
diff -r 92dfcfb03add -r 5569a3f066cf topGO.xml
--- a/topGO.xml	Wed Aug 22 10:39:30 2018 -0400
+++ b/topGO.xml	Wed Sep 12 10:01:35 2018 -0400
@@ -1,11 +1,16 @@
-<tool id="topGO" name="topGO" version="2018.08.22">
+<tool id="topGO" name="topGO" version="2018.09.12">
     <description>
     Enrichment analysis for Gene Ontology
     </description>
     <requirements>
-        <requirement type="package" version="3.4.1">R</requirement>
-        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
+        <requirement type="package" version="3.5.0">R</requirement>
+        <requirement type="package" version="3.0.0">r-ggplot2</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement>
         <requirement type="package" version="1.56.0">bioconductor-graph</requirement>
         <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
         <requirement type="package" version="3.5.0">bioconductor-go.db</requirement>