Can't see the y axis on the enrichmentDotPlot

[aeeckhou]

Hello,

I am trying to vizualize my results of enrichment with a dotplot with the code below :

query <- bedToGranges(narrow_peak_files)
table_enrichment = enrichment(query, catalog, byChrom = FALSE)
pdf("dotplot.pdf"))
enrichmentDotPlot(table_enrichment)
dev.off()

But the y axis is cropped.

Heterozygote_SPI1_QE_Follicular_R1.mLb.clN_peaks.narrowPeak_dotplot_normal.pdf

I tried to play around pdf() and look online for other solution, but I can't find any right now. Do you have a solution for this problem ?

Best,
Alexandre

[sarahhp]

I've been having the same issue and found for 2022 non-redundant set I needed to abbreviate the category to only include the transcription factors. Then I plotted a similar thing in ggplot:

enrichment.df$transcription_factor = gsub(":.*","", enrichment.df$category)
ggplot(enrichment.df[1:20,], aes(x=mapped.peaks.ratio, y=transcription_factor, colour=q.significance, size=nb.overlaps)) +
geom_point() +theme_bw() + scale_colour_distiller(palette="RdBu")