Description Usage Arguments Value Examples
Visualize hyp/multihyp objects as a dots plot
1 2 3 4 5 6 7 8 9 10 11 |
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 |
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
1 2 3 4 5 6 7 8 9 | 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")
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