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,
  measure = c("tf", "tfidf"),
  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.

measure

a character, specifying how frequencies should be computed. "tf" uses term frequencies and "tfidf" (default) applies inverse document frequency weights to term frequencies.

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' = 1:10, 'g2' = 11:20)
plotMsigWordcloud(hgsc, groups, rmwords = getMsigBlacklist())


[Package vissE version 1.0.0 Index]