plot_pca: Plot PCA results

In nchlis/pca.utils: R package for easy plotting of PCA results

Description

inputs:

Usage

plot_pca(x, npcs = c(1, 2), xlab = NULL, ylab = NULL, zlab = NULL,
  main = "PCA results", pch = NULL, col = NULL, bg = NULL, cex = NULL,
  pal = RColorBrewer::brewer.pal(8, "Dark2"), add.legend = FALSE,
  legend.position = "bottomleft", legend.text = NULL, legend.col = NULL,
  legend.bg = NULL, legend.inset = 0, ...)

Arguments

x:	data frame, matrix or prcomp object to plot.
npcs:	numeric vector indicating PCs to plot, defaults to c(1,2). If length(npcs)>3, only the first 3 elements will be used.
xlab:	xlabel, see par.
ylab:	ylabel, see par, see par.
zlab:	zlabel, see plot3d.
main:	title for the plot, see par. Defaults to 'PCA results'.
pch:	numeric vector of plotting characters, see par.
col:	vector of plotting character colors, see par.
bg:	vector of plotting character background colors, see par.
cex:	plotting character size. Defaults to 1 for 2D and to 7 for 3D plots.
pal:	color palette. Defaults to the colorblind friendly RColorBrewer::brewer.pal(8,"Dark2"). Setting pal to NULL, will lead to the default R colors being used in the plots.
add.legend:	add a legend to the plot, defaults to FALSE.
legend.position:	, argument to legend. Position of the legend in the plot, defaults to 'bottomleft'.
legend.text:	character vector to appear in the legend.
legend.col:	color of legend elements, defaults to unique(col)
legend.bg:	background color of legend elements, defaults to unique(bg)
legend.inset:	inset distance(s) from the margins as a fraction of the plot region when legend is placed by keyword
...:	arguments passed to the plot() or rgl::plot3d() functions

Value

a list with class "prcomp", containing the same elements as prcomp:

• var_explained: numeric vector indicating the varince explained by each PC

Examples

data(iris)

# 2D PCA
plot_pca(x=iris[1:4],col=iris$Species)

# 3D PCA
plot_pca(x=iris[1:4],npcs=3,col=iris$Species)

nchlis/pca.utils documentation built on May 23, 2017, 11:33 a.m.