hyp_plot {hypeR}R Documentation

Visualize top enriched pathways

Description

Visualize top enriched pathways

Usage

hyp_plot(df, top = 10, val = c("fdr", "pval"))

Arguments

df

A hyper dataframe

top

Limit number of pathways shown

val

Choose significance value e.g. c("pval", "fdr")

Value

A plotly object

Examples

# 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")
[Package hypeR version 1.00.0 Index]