gsea_heatmap {SCdeconR}

Heatmap to demonstrate enrichment of selected gene-sets

Description

Heatmap to demonstrate enrichment of selected gene-sets.

Usage

gsea_heatmap(
  normdata,
  teststats,
  gmtfile,
  numgenes,
  gsname_up,
  gsname_down,
  anncol,
  color,
  anncolors = NULL,
  rankcol = TRUE,
  zscore_range = c(-3, 3)
)

Arguments

normdata

a matrix-like object of normalized & untransformed bulk RNA-seq data, with rows representing genes and columns representing samples. The first element of the output from function run_de.

teststats

a data.frame containing differential expression results with five columns: "Gene name", "log2 fold change", "log2 average expression", "p value", "adjusted p value". The second element of the output from function run_de.

gmtfile

path to gmt file used for GSEA analysis.

numgenes

Number of genes to include in the heatmap. Will choose numgenes # of top up-regulated genes, as well as numgenes # of down-regulated genes

gsname_up

a character value indicating selected up-regulated gene-set.

gsname_down

a character value indicating selected down-regulated gene-set.

anncol

a data.frame of sample meta information to include as column annotation bars. See option annCol from aheatmap for more details.

color

color used for heatmap. See option color option from aheatmap for details.

anncolors

optional data.frame to define colors for column annotations in anncol.

rankcol

a logical value indicating whether to sort samples based on correlation between fold change & gene expression for better visualization. Default to TRUE.

zscore_range

a vector of length two indicating the desired range of z-score transformed data. Default to c(-3, 3).

Details

this function does not support output from GSEA R implementation

Value

a heatmap outputted from aheatmap function from NMF package