cgapsPlot: Plot Individual CoGAPS Patterns

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

Plot Individual CoGAPS Patterns

Description

Function to plot each pattern of the pattern matrix from a cogapsResult and color by cell classifier information to identify which patterns identify which cell classes.

Usage

cgapsPlot(
  cgaps_result,
  sample.classifier,
  cols = NULL,
  sort = TRUE,
  patterns = NULL,
  matrix = FALSE,
  ...
)

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)
cols	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
...	addition arguments to plot function

Value

Series of plots of pattern matrix patterns colored by cell classifications

Examples

data("schepCogapsResult")
data(schepCellTypes)

cgapsPlot(schepCogapsResult, schepCellTypes)

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