plot_pca_projection_labeloptions: Plot PCA projection and data points from original PCA

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

Plot PCA projection and data points from original PCA

Description

Plots projection from rotated.scores file (output of intersect_do_PCA_and_project_second_dataset) on top of original data

Usage

plot_pca_projection_labeloptions(
  file,
  rotated.file,
  info.name,
  info.type,
  info.name2,
  info.type2,
  title = "Projection",
  labelsProj = T,
  labelsOrgPCA = F,
  PCx = "PC1",
  PCy = "PC2",
  ellipse = F,
  conf = 0.95,
  fliph = F,
  flipv = F,
  save = F,
  savename = ""
)

Arguments

file	scores file of original data
rotated.file	File containing scores matrix of projected data
info.name	Vector of sample names in original PCA
info.type	Vector of sample types in original PCA in the same order as names
info.name2	Vector of sample names of projected data
info.type2	Vector of sample types of projected data in the same order
title	Title of the plot
labelsProj	default=T
labelsOrgPCA	default=F
PCx, PCy	PCs to display
ellipse	Construct confidence region based on groups in info.type, default = T
conf	default = 0.95
fliph, flipv	flip plot hoirzontally or vertically
save	save plot as png
savename	name of file saved

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