plotMsigWordcloud {vissE} | R Documentation

## Compute and plot word frequencies for multiple MSigDB collections

### Description

Given a gene set collection, this function computes the word frequency of gene set names from the Molecular Signatures Database (MSigDB) collection (split by _). Word frequencies are also computed using short descriptions attached with each gene set object.

### Usage

    plotMsigWordcloud(
      msigGsc,
      groups,
      weight = NULL,
      measure = c("tfidf", "tf"),
      version = msigdb::getMsigdbVersions(),
      org = c("auto", "hs", "mm"),
      rmwords = getMsigBlacklist(),
      type = c("Name", "Short")
    )

### Arguments

`msigGsc` | a GeneSetCollection object, containing gene sets from the MSigDB. The `GSEABase::getBroadSets()` function can be used to parse XML files downloaded from MSigDB.
`groups` | a named list, of character vectors or numeric indices specifying node groupings. Each element of the list represent a group and contains a character vector with node names.
`weight` | a named numeric vector, containing weights to apply to each gene-set. This can be -log10(FDR), -log10(p-value) or an enrichment score (ideally unsigned).
`measure` | a character, specifying how frequencies should be computed. "tf" uses term frequencies and "tfidf" (default) applies inverse document frequency weights to term frequencies.
`version` | a character, specifying the version of msigdb to use (see `msigdb::getMsigdbVersions()`).
`org` | a character, specifying the organism to use. This can either be "auto" (default), "hs" or "mm".
`rmwords` | a character vector, containing a blacklist of words to discard from the analysis.
`type` | a character, specifying the source of text mining. Either gene set names (`Name`) or descriptions (`Short`) can be used.

### Value

a ggplot object.

### Examples

    data("hgsc")
    groups <- list('g1' = names(hgsc)[1:25], 'g2' = names(hgsc)[26:50])
    plotMsigWordcloud(hgsc, groups, rmwords = getMsigBlacklist())

[Package vissE version 1.2.2 Index]