plotPCA: Principle component analysis (PCA) or multidimensional...

In AlexGa/GraftingScripts: Reproducible scripts for studying the graft formation

Description

Plot samples on a two-dimensional scatterplot in which the distances on the plot indicate the expression differences between the samples

Usage

plotPCA(exp_data, groups, do.legend=F, plot_time_points=F, log=T, do.MDS=F, cols=NULL, epsilon = 1, return_plotMatrix = FALSE, ...)

Arguments

exp_data	expression matrix, columns represent the samples and rows the genes (or transcripts)
groups	numeric vector describing the relationships of columns to certain groups (like biological replicates)
do.legend	boolean value defining if a color legend should be ploted
plot_time_points	boolean value indicating if the grafting time points shall be plotted
log	boolean value defining if the expression data should be log transformed before the calculation of PCA or MDS
do.MDS	boolean value defines if PCA or MDS should be calculated. Default: TRUE
cols	character vector defining the colors to use for the different samples
epsilon	numeric value indicates pseudocount used if log=TRUE
return_plotMatrix	boolean value indicates if PCA or MDS results should be returned
...	optional plot parameters plot

Value

a matrix

Author(s)

Alexander Gabel

AlexGa/GraftingScripts documentation built on May 26, 2019, 9:34 a.m.