org.db bug in gotangram

[igumnov-daniel]

Hi!

I'm trying to plot "gotangram" for GO BP enriched A.thaliana data. Other types like bar, upset, and the network worked fine, but gotangram is raising an error: "Error: Bioconductor orgdb for org.At.eg.db not found. You should install first.". It looks like a bug since for A.thaliana it's org.At.tair.db

test <- c('AT1G12610', 'AT5G47600', 'AT1G33760') # just to make it easy to reproduce
gs <- getGO(org="Arabidopsis thaliana", ont="bp")
go_bp <- genORA(test,geneset=gs) 
plotEnrich(go_bp, plot_type = "gotangram", sim_method = "Rel", org='Arabidopsis thaliana')

ps Many thanks for the package. I do love it.

[reedliu]

@igumnov-daniel Thanks for your report. This is a bug in querying At org db. Now please update the tool from GitHub and you would find it works now. :)

packageVersion('genekitr')  # 1.0.9
test <- c('AT1G12610', 'AT5G47600', 'AT1G33760') # just to make it easy to reproduce
gs <- getGO(org="Arabidopsis thaliana", ont="bp")
go_bp <- genORA(test,geneset=gs) 
plotEnrich(go_bp, plot_type = "gotangram", sim_method = "Rel", org='Arabidopsis thaliana')

[igumnov-daniel]

Lovely! Many thanks for the rapid fix 👍🏻