generate_pca_plots: generate PCA plots

In anthony-aylward/exploreatacseq: Exploratory Analysis of ATAC-seq data

Description

plot PCA of the read counts

Usage

generate_pca_plots(
  counts,
  output_prefix,
  treatment = NULL,
  treatment_order = NULL,
  treatment_groups = list(),
  labels = FALSE,
  palette_order = "categorical",
  palette = NULL
)

Arguments

counts	matrix of read counts
output_prefix	prefix for output files
treatment	character vector indicating treatment, if NULL, it will be inferred from the read count matrix
treatment_order	order of treatments WRT the palette
treatment_groups	list of treatment groups
labels	if TRUE, text labels will be added to points in all plots
palette_order	ordering of color palette, eithier "categorical" or "sequential"
palette	the color palette

anthony-aylward/exploreatacseq documentation built on May 10, 2021, 8:45 a.m.