plot_varimax_paint_gene: Plot varimax PCA Paint Gene

In graeberlab-ucla/glab.library: Data Analysis Functions

Plot varimax PCA Paint Gene

Description

Plots varimax PCA from scores file (output of PCA_from_file followed by varimax_from_file)

Usage

plot_varimax_paint_gene(
  file,
  info.name,
  info.type,
  gene,
  title = "",
  labels = TRUE,
  PCx = "PC1",
  PCy = "PC2",
  ellipse = F,
  conf = 0.95,
  density = F,
  fliph = F,
  flipv = F,
  missing = "plot"
)

Arguments

file	File containing scores matrix
info.name	Vector of sample names
info.type	Vector of sample types in the same order
title	Title of the plot
labels	default=T
PCx, PCy	PCs to display
ellipse	Construct confidence region based on groups in info.type, default = T
conf	default = 0.95
density	plot x-y density plots
fliph, flipv	flip plot hoirzontally or vertically
missing	plot, plot.grey90 or do.not.plot points with missing gradient fill values (grey90 is lighter than the default grey) NEED TO CHECK/TEST IF THESE ARE NEEDED

Details

plot_varimax_paint_gene differs from plot_varimax in that it uses gradient coloring of points based on the expression values of a gene

graeberlab-ucla/glab.library documentation built on Oct. 28, 2024, 10:48 a.m.