heatmapPatternMatrix: Plot the patternMatrix as a heatmap

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

Plot the patternMatrix as a heatmap

Description

Selects the pattermMatrix (patterns by cells) from the CoGAPSResult and plots the data as a heatmap. Intended to visualize the celltypes distinguished by the patterns found by CoGAPS.

Usage

heatmapPatternMatrix(
  cgaps_result,
  sample.classifier,
  cellCols = NULL,
  sort = TRUE,
  patterns = NULL,
  matrix = FALSE,
  rowColors = NULL,
  ...
)

Arguments

cgaps_result	CoGAPSResult object from a CoGAPS run or the pattern matrix (matrix must be set equal to TRUE in the latter case)
sample.classifier	factor of sample classifications for all cells for the data to be plotted by (e.g. celltypes)
cellCols	vector of colors to be used for the cell classes; should have the same number of colors as levels of the sample.classifier factor. If left null a list of colors is produced
sort	TRUE if samples will be sorted according to sample.classifier prior to plotting
patterns	numerical vector of patterns to be plotted; if null all patterns are plotted
matrix	if false cgaps_result is interpreted as a CoGAPSResult object, if true it is interpreted as the pattern matrix being input directly
rowColors	vector of colors to plot along patterns, if NULL generated automatically
...	additional arguments to the heatmap.2 function

Value

Heatmap of patternMatrix with color labels for samples

Examples

data("schepCogapsResult")
data(schepCellTypes)

heatmapPatternMatrix(schepCogapsResult, sample.classifier = schepCellTypes)

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.