plotGeneStats {vissE} | R Documentation

## Plot gene statistics for clusters of gene sets

### Description

This function plots gene statistics against gene frequencies for any given cluster of gene sets. The plot can be used to identify genes that are over-represented in a cluster of gene-sets (identified based on gene-set overlaps) and have a strong statistic (e.g. log fold-chage or p-value).

### Usage

    plotGeneStats(
      geneStat,
      msigGsc,
      groups,
      statName = "Gene-level statistic",
      topN = 5
    )

### Arguments

`geneStat` | a named numeric, containing the statistic to be displayed. The vector must be named with either gene Symbols or Entrez IDs depending on annotations in msigGsc.
`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.
`statName` | a character, specifying the name of the statistic.
`topN` | a numeric, specifying the number of genes to label. The top genes are those with the largest count and statistic.

### Value

a ggplot object, plotting the gene-level statistic against gene frequencies in the cluster of gene sets.

### Examples

    library(GSEABase)

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

    #create statistics
    allgenes = unique(unlist(geneIds(hgsc)))
    gstats = rnorm(length(allgenes))
    names(gstats) = allgenes

    #plot
    plotGeneStats(gstats, hgsc, groups)

[Package vissE version 1.2.2 Index]