plot_pca_gradient_fill_repel: Plot PCA Gradient Fill

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

Plot PCA Gradient Fill

Description

Plots PCA from scores file (output of PCA_from_file)

Usage

plot_pca_gradient_fill_repel(
  file,
  info.name,
  info.type,
  info.color,
  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
info.color	Vector to be used for gradient fill of plot points, with 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)

Details

plot_pca_gradient_fill differs from plot_pca in that it uses gradient-based coloring of points plot_pca_gradient_fill_repel uses geom_text_repel

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