plotGeneStats {vissE} | R Documentation |
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).
plotGeneStats( geneStat, msigGsc, groups, statName = "Gene-level statistic", topN = 5 )
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 |
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. |
a ggplot object, plotting the gene-level statistic against gene frequencies in the cluster of gene sets.
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)