hyp_plot {hypeR} | R Documentation |
Visualize top enriched pathways
hyp_plot(df, top = 10, val = c("fdr", "pval"))
df |
A hyper dataframe |
top |
Limit number of pathways shown |
val |
Choose significance value e.g. c("pval", "fdr") |
A plotly object
# Grab a list of curated gene sets REACTOME <- ex_get("C2.CP.REACTOME") # Genes involed in tricarboxylic acid cycle symbols <- 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 <- hypeR(symbols, REACTOME, bg=2522, fdr=0.05) # Visualize hyp_plot(hyp, top=3, val="fdr")