seekGSEbubble: bubbleplot for GSEAs

In Solatar/seeqR:

Description

Imports: ggplot2

Usage

seekGSEbubble(gsealist, minoverlap = 1, pcutoff = 0.05)

Arguments

gsealist	list of gsea tables, obtained from seekGSEA() function from this package
minoverlap	minimum number of sets that have to have this enriched term (significant or not)
pcutofft	p value cutoff by which pathways are discarded in the beginning. Usefull if the "arguments imply differing number of rows" error comes up which means that some items in the list have no row either due to the pvalue filtering (set this to 1 then) or because they didn't have it to begin with (in that case, exclude the itemfrom the list)

Value

a ggplot object; seethrough dots have p>0.05 (not significant)

Examples

myDE1 <- sqDE
rl1 <- seekGSErl(myDE1, pFilter=0.05, colentrez="EntrezId")
mygsea1 <- seekGSEA(rl1, Species="mouse", Ont="BP")
myDE2 <- sqDE
rl2 <- seekGSErl(myDE2, pFilter=0.05, colentrez="EntrezId")
mygsea2 <- seekGSEA(rl2, Species="mouse", Ont="BP")
seekGSEbubble(list(g1=mygsea1, g2=mygsea2), 2)

Solatar/seeqR documentation built on Feb. 19, 2021, 8:07 p.m.