log-10 transformation introduced infinite values

[abeedhakhan]

How can I deal with these warning while plotting heatplot after GO enrichment analysis? I think this is also not letting the fold change colors appear on the plots. Kindly help.

print(heatplot(ego, foldChange=geneList, showCategory = 5) +

•     ggtitle(paste(comp, "CC", sep = " - ")) +
  

•     theme(axis.text.y = element_text(size = 8)))
  

Warning messages:
1: In (function (name = waiver(), ..., low = muted("red"), mid = "white", :
log-10 transformation introduced infinite values in midpoint.
2: In transformation$transform(x) : NaNs produced
3: In (function (name = waiver(), ..., low = muted("red"), mid = "white", :
log-10 transformation introduced infinite values.

Thanks in advance.
Abeedha

[guidohooiveld]

Your code as such (using the example data) is working in my hands. See below.

So your issue is specific to your input. Based on the warning it seems values of zero are log-transformed, which obviously not possible.

If your problem persists, are you able to share you full code and/or input?

> library(enrichplot)
> library(DOSE)
> library(ggplot2)
> 
> data(geneList)
> de <- names(geneList)[1:100]
> x <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)

> heatplot(x, foldChange=geneList, showCategory = 5) + 
+     ggtitle(paste("comp", "BP", sep = " - ")) +
+     theme(axis.text.y = element_text(size = 8))
>

[abeedhakhan]

The difference column in my data is already logFC from which I make the geneList (not just fold change). Could that be causing a problem while plotting since the plotting is trying to log-10 transform it again?