hyp_emap {hypeR} | R Documentation |
Visualize hyp/multihyp objects as an enrichment map
hyp_emap(hyp_obj, title = "", similarity_metric = c("jaccard_similarity", "overlap_similarity"), similarity_cutoff = 0.2, 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 |
similarity_metric |
Metric to calculate geneset similarity |
similarity_cutoff |
Geneset similarity cutoff |
pval_cutoff |
Filter results to be less than pval cutoff |
fdr_cutoff |
Filter results to be less than fdr cutoff |
val |
Choose significance value shown above 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 |
An option to show plots |
return_plots |
An option to return plots |
A visNetwork object or list of visNetwork objects
gsets <- hyperdb_fetch(type="gsets", "KEGG_2019_Human") 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, gsets, bg=2522, fdr_cutoff=0.05) # Visualize hyp_emap(hyp_obj, top=30, val="fdr")