ctlab / fgsea

Fast Gene Set Enrichment Analysis
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Setting colwidth to zero doesn't seem to work properly #21

Closed konsolerr closed 6 years ago

konsolerr commented 6 years ago

Hi @assaron,

Setting colwidth to zero doesn't seem to work as expected: expected behavior would be not drawing the column at all. Please, see the example below:

library(data.table)
library(fgsea)
library(ggplot2)

data(examplePathways)
data(exampleRanks)

fgseaRes <- fgsea(pathways = examplePathways, 
                  stats = exampleRanks,
                  minSize=15,
                  maxSize=500,
                  nperm=10000)

topPathwaysUp <- fgseaRes[ES > 0, ][head(order(pval), n=10), pathway]
topPathwaysDown <- fgseaRes[ES < 0, ][head(order(pval), n=10), pathway]
topPathways <- c(topPathwaysUp, rev(topPathwaysDown))
plotGseaTable(examplePathways[topPathways], exampleRanks, fgseaRes, 
              gseaParam = 0.5, colwidths = c(0, 1, 0.5, 0.5, 0))

And after you plot GSEA table you can easily see "leftovers" on the most left and most right columns. image

Cheers and best of luck Konstantin