| hyp_hmap {hypeR} | R Documentation |
Visualize hyp/multihyp objects as a hiearchy map
hyp_hmap(hyp_obj, title = "", pval_cutoff = 1, fdr_cutoff = 1,
val = c("fdr", "pval"), top = NULL, multihyp_titles = TRUE,
show_plots = TRUE, return_plots = FALSE)
hyp_obj |
A hyp or multihyp object |
title |
Plot title |
pval_cutoff |
Filter results to be less than pval cutoff |
fdr_cutoff |
Filter results to be less than fdr cutoff |
val |
Choose significance value displayed when hovering nodes e.g. c("fdr", "pval") |
top |
Limit number of pathways shown |
multihyp_titles |
Use false to disable plot titles for multihyp objects |
show_plots |
Use true to show plots |
return_plots |
Use true to return plots |
A visNetwork object or list of visNetwork objects
rgsets <- hyperdb_fetch(type="rgsets", "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")
# Perform hyper enrichment
hyp_obj <- hypeR(signature, rgsets, bg=2522, fdr_cutoff=0.05)
# Visualize
hyp_hmap(hyp_obj, top=60)