guidohooiveld
commented
3 months ago So you basically would like to have a plot in which the ratios (e.g. 9/81) are displayed as fraction (0.111)?
First of all, I don't know why the function dotplot seems to sometimes plot ratios, and other times fractions...
Yet, a simple (but not a really elegant) solution would be to first manually convert the ratios to fractions before plotting. This is just adding a single line of code:
ego.combined@compareClusterResult$GeneRatio <- sapply( strsplit(ego.combined@compareClusterResult$GeneRatio, "/"),
function(x) as.numeric(x[1])/as.numeric(x[2]) )Example:
> library(clusterProfiler)
> library(enrichplot)
> library(org.Hs.eg.db)
>
> data(geneList, package="DOSE")
> genes.up <- names(geneList)[geneList > 2]
> genes.down <- names(geneList)[geneList < -2]
>
>
> up <- enrichGO(gene = genes.up,
+ universe = names(geneList),
+ OrgDb = org.Hs.eg.db,
+ ont = "ALL",
+ pAdjustMethod = "BH",
+ pvalueCutoff = 0.05,
+ qvalueCutoff = 0.05,
+ readable = TRUE)
>
>
> down <- enrichGO(gene = genes.down,
+ universe = names(geneList),
+ OrgDb = org.Hs.eg.db,
+ ont = "ALL",
+ pAdjustMethod = "BH",
+ pvalueCutoff = 0.05,
+ qvalueCutoff = 0.05,
+ readable = TRUE)
>
>
> ego.up <- pairwise_termsim(up, showCategory=30)
> ego.up <-simplify(ego.up, cutoff=0.7, by="p.adjust", select_fun=min)
>
>
> ego.down <- pairwise_termsim(down, showCategory=30)
> ego.down <-simplify(ego.down, cutoff=0.7, by="p.adjust", select_fun=min)
>
> ego.list<-list("activated"=ego.up, "suppressed"=ego.down)
> ego.combined <- merge_result(ego.list)
>
>
> ## plot with ratio
> dotplot(ego.combined,split="Cluster", showCategory=15, x="GeneRatio",
+ size= "count", font.size=7, label_format=10) +
+ facet_grid(.~Cluster) +
+ ggtitle("GO ORA, displaying ratios")
> >
> ## manually convert ratios into fractions
> ego.combined@compareClusterResult$GeneRatio <- sapply( strsplit(ego.combined@compareClusterResult$GeneRatio, "/"),
+ function(x) as.numeric(x[1])/as.numeric(x[2]) )
>
> ## plot with fraction
> dotplot(ego.combined,split="Cluster", showCategory=15, x="GeneRatio",
+ size= "count", font.size=7, label_format=10) +
+ facet_grid(.~Cluster) +
+ ggtitle("GO ORA, displaying fractions")
>
GuangchuangYu
nina-hahn
Dear all,
in some dotplots the GeneRatio is presented as a number.
After applying pairwise_termsim and simplify, it is presented as a fraction.
How can I change the plots to show always a number as GeneRatio? Both plots originate from CompareCluster results.
Here is the code of the second plot . The first just skips the pairwise_termsim and simplify functions `ego.down<-enrichGO(gene= DEGs.down$ENSEMBL, OrgDb = organism, ont= "All", pAdjustMethod = "BH", pvalueCutoff = 0.05, qvalueCutoff = 0.05, keyType = "ENSEMBL", readable = TRUE)
ego.down<-pairwise_termsim(ego.down, showCategory=30) ego.down<-simplify(ego.down,cutoff=0.7, by="p.adjust", select_fun=min)
ego.up<-enrichGO(gene= DEGs.up$ENSEMBL, OrgDb = organism, ont= "All", pAdjustMethod = "BH", pvalueCutoff = 0.05, qvalueCutoff = 0.05, keyType = "ENSEMBL", readable = TRUE)
ego.up<-pairwise_termsim(ego.up, showCategory=30) ego.up<-simplify(ego.up,cutoff=0.7, by="p.adjust", select_fun=min)
ego.list<-list("activated"=ego.up, "suppressed"=ego.down) ego.combined<-merge_result(ego.list)
options(enrichplot.colours = c("#009E73","#f0e442"))
dotplot(ego.combined,split="Cluster", showCategory=15, x="GeneRatio", size= "count", font.size=10, label_format=60) + facet_grid(.~Cluster)+ ggtitle("GO ORA") `
Best, Nina