hyp_dots {hypeR} | R Documentation |
Visualize hyp/multihyp objects as a dots plot
hyp_dots( hyp_obj, top = 20, abrv = 50, sizes = TRUE, pval = 1, fdr = 1, val = c("fdr", "pval"), title = "", merge = FALSE )
hyp_obj |
A hyp or multihyp object |
top |
Limit number of genesets shown |
abrv |
Abbreviation length of geneset labels |
sizes |
Size dots by geneset sizes (if merge=TRUE, size dots by significance) |
pval |
Filter results to be less than pval cutoff |
fdr |
Filter results to be less than fdr cutoff |
val |
Choose significance value for plot e.g. c("fdr", "pval") |
title |
Plot title |
merge |
Use true to merge a multihyp object into one plot |
A ggplot object
genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG") signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502", "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC", "IDH2","IDH1","OGDHL","PC","SDHA","SUCLG1","SUCLA2","SUCLG2") hyp_obj <- hypeR(signature, genesets, background=2522) hyp_dots(hyp_obj, val="fdr")