hyp_hmap {hypeR} | R Documentation

## Visualize hyp/multihyp objects as a hiearchy map

### Description

Visualize hyp/multihyp objects as a hiearchy map

### Usage

    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)

### Arguments

`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

### Value

A visNetwork object or list of visNetwork objects

### Examples

    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)

[Package hypeR version 1.3.0 Index]