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]