error in enrichmentPlot() when providing a partially empty GO object

[spribitzer]

I recently encountered an error during a call to enrichmentPlot():

> x <- getEnrichedGO(annotatedPeakList, orgAnn="org.Hs.eg.db", condense=TRUE)
> enrichmentPlot(x)
Error in `[.data.frame`(.ele, !is.na(.ele$pvalue), c(cn.id, cn.term, "pvalue",  :  undefined columns selected

Upon investigation I noticed that one of the list items in x was an empty dataframe:

> x$mf
 [1] go.id              go.term            Definition         Ontology           count.InDataset   
 [6] count.InGenome     pvalue             totaltermInDataset totaltermInGenome  EntrezID          
<0 rows> (or 0-length row.names)

I could successfully plot with enrichmentPlot() by adding a row of NAs:

> x$mf[nrow(x$mf)+1,] <- NA
> enrichmentPlot(x)

It might be worth adding a test for an empty df into enrichmentPlot(), e.g. similar to this:

for (item in c("bp", "mf", "cc")) {
     if (nrow(x[[item]]) == 0) {
      x[[item]][nrow(x[[item]])+1,] <- NA
    }
}

[jianhong]

Thank you for reporting this and kindly give the solutions. I will fix the issue as soon as possible.