spinning_3d_pca_link: Plot PCA scores in 3d space. Link to locally saved 3d html...

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

Plot PCA scores in 3d space. Link to locally saved 3d html plot gets made and opens automatically in browser after function is run.

Description

Plot PCA scores in 3d space. Link to locally saved 3d html plot gets made and opens automatically in browser after function is run.

Usage

spinning_3d_pca_link(
  scores,
  info.type,
  X = PC1,
  Y = PC2,
  Z = PC3,
  title = "3d PCA plot",
  colorlst = NULL,
  marker = NULL
)

Arguments

scores;	the output from PCA_from_file that has been read in using read.delim - first column includes the samples
info.type;	info.type column is in the same order as samples in scores and is a factor. Points will be colored by info.type. It is recommended to make info.type a new column in the scores file.
X;	default is PC1
Y;	default is PC2
Z;	default is PC3
title;	title name for 3d plot and the name that is used in saving the html file
colorlst;	optional: list of colors that correspond to the unique(info.type)
marker;	optional: can use this parameter to adjust size, shape, opacity of points

Value

html link to 3d Spinning PCA plot

Examples

my_PCA_scores <- read.delim("my_PCA_scores.txt")
my_PCA_scores$type <- info$type[match(my_PCA_scores$Score, info$sample)]
my_PCA_scores$type <- factor(my_PCA_scores$type, levels = unique(my_PCA_scores$type))
spinning_3d_pca_link(scores = my_PCA_scores, info.type = my_PCA_scores$type, X = my_PCA_scores$PC1, Y = my_PCA_scores$PC2, Z = my_PCA_scores$PC3, title = "3d PCA plot", colorlst=c("red", "dodgerblue", "pink", "orange"))

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