PCAplot.cds: Pairwise Principal Component Analysis Plots of CountDataSet...

In hbc/CHBUtils: "Useful utility functions used at the core"

Description

Pairwise Principal Component Analysis Plots of CountDataSet objects

Usage

PCAplot.cds(countdataset, categories, categories2, title, colorpalette,
  alpha = 1, numcomponents = 4, normalize.counts = TRUE)

Arguments

countdataset	CountDataSet, required
categories	character string, column header of column containing different categories to highlight with colors, required
categories2	character string, column header of column containing different categories to highlight with shapes, optional
title	character string, title for the plot, required
colorpalette	charcter vector of RGB colors (long enough for a color per category), required
alpha	alpha shading from 0 (transparent) to 1 (opaque), defaults to 1
numcomponents	number of principal components to plot, defaults to 4

Value

pairwise plots of samples plotted by principal component

See Also

pair which this function uses to plot all pairwise combos

Examples

PCAplot.cds(countdataset=cds, categories="condition", title="PCAplot", colorpalette=c("#FF0000", "#00FF00", "#0000FF"), alpha=0.8, numcomponents=4)

hbc/CHBUtils documentation built on May 17, 2019, 3:07 p.m.