mitoTreeHeatmap: Circular heatmap on mitochondrial gene set tree.

In CaluraLab/mitology: Study of mitochondrial activity from RNA-seq data

Circular heatmap on mitochondrial gene set tree.

Description

Given a matrix of scores, it returns a circular heatmap of the mitochondrial gene sets (leaf of the database tree) or gene set groups (section of the database tree).

Usage

mitoTreeHeatmap(
  data,
  database = "MitoCarta",
  sections = FALSE,
  samples = NULL,
  labelNames = "sections",
  ...
)

Arguments

data	matrix or data.frame with samples in columns and mitochondrial gene sets in rows.
database	character string saying the database used for the analysis. Either one of "MitoCarta", "Reactome", "GO-CC" and "GO-BP".
sections	logical. Either to keep the aggregated gene set categories or the specific gene sets. Default is FALSE.
samples	character vector with the names of samples to be plotted. Otherwise all samples are plotted.
labelNames	character string that says to plot either the names of "sections" or "leaves".
...	other arguments passed on to the gheatmap function.

Value

A ggplot object.

Examples

MClist <- getGeneSets()
n <- length(names(MClist)) * 5
rmatrix <- matrix(rnorm(n, 0), ncol = 5)
rownames(rmatrix) <- names(MClist)
colnames(rmatrix) <- paste0("Sample_", seq_len(5))
mitoTreeHeatmap(data = rmatrix, database = "MitoCarta")

CaluraLab/mitology documentation built on April 14, 2025, 8:26 a.m.