PCAPlots: PCA Plots

In brightchan/cjbmisc:

Description

A group of functions for PCA plots.

• pca: PCA plot with one or two group info.

• pca_multi: Multiple PCA plots for top PCs.

• pca_bg: PCA plot with color background shading for each subtype

Usage

pca(
  df,
  A,
  B = NULL,
  title = "PCA",
  col = colpal,
  nameA = "subtypeA",
  nameB = "subtypeB",
  point.size = 4,
  shapes = c(16:18, 15),
  plot.it = TRUE,
  return.data = FALSE
)

pca_multi(
  df,
  subtype = NULL,
  n = 6,
  col = colpal,
  title = NULL,
  plot.it = TRUE
)

pca_bg(
  df,
  subtype,
  col = colpal,
  legend.name = NULL,
  point.size = 6,
  text.size = 26,
  mar = 15,
  plot.it = TRUE
)

Arguments

df	numeric dataframe with rows of samples and columns of features
A, B, subtype	character vector of the subtypes of samples
col	color to be used for each subtype.
plot.it	if FALSE, no plot printed, only return the plot object
n	for pca_multi, number of PCs to be plotted
mar	for pca_bg, margin between the points to the frame.
"+"	use + to add ggplot layers for more customization

Value

Print the plot and return the plot

• pca: a ggplot object

• pca_multi: a plot object

See Also

autoplot and prcomp

brightchan/cjbmisc documentation built on Nov. 5, 2021, 4:12 p.m.