Can't see the y axis on the enrichmentDotPlot

remap-cisreg / ReMapEnrich

ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

http://remap-cisreg.github.io/ReMapEnrich

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Can't see the y axis on the enrichmentDotPlot #19

Open aeeckhou opened 1 year ago

aeeckhou commented 1 year ago

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 commented 11 months ago

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")