Mercurial > repos > proteore > proteore_topgo
changeset 1:5569a3f066cf draft
planemo upload commit dd5bd9c90796d9d9a0f62992bb5ca33b0efe6a05-dirty
| author | proteore |
|---|---|
| date | Wed, 12 Sep 2018 10:01:35 -0400 |
| parents | 92dfcfb03add |
| children | 02558d6a391c |
| files | enrichment_v3.R topGO.xml |
| diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- 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") }
--- 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>