This function generates PCA plot from counts, FPKM and TPM tables from rnaseqCounts outuputs.

pca(
experiment.table = "./_counts.txt",
type = c("counts", "FPKM", "TPM"),
covariatesInNames = FALSE,
samplesName = TRUE,
principal.components = c(1, 2),
legend.position = c("bottom", "bottomleft", "left", "topleft", "top", "topright",
"right", "center"),
pdf = TRUE,
output.folder = getwd()
)

## Arguments

experiment.table, a character string indicating the counts, FPKM or TPM table file name and its path a character value indicating the content of the file: counts, FPKM or TPM a boolean value indicating if covariates are inserted after \_ in the filename a boolean value indicating if in the plot samples names are plotted or not a numerical vector with two values indicating the principal components to be plotted a character string indicating the location of the covariates legend a boolean value indicating if results has to be saved in a pdf output folder

## Value

Returns a PCA plot

## Examples

if (FALSE) {
system("wget 130.192.119.59/public/test.analysis.zip")
unzip("test.analysis.zip")
setwd("test.analysis")
library(docker4seq)
pca(experiment.table="./_log2FPKM.txt", type="FPKM",
legend.position="topleft", covariatesInNames=FALSE, samplesName=TRUE,
principal.components=c(1,2), pdf = TRUE,
output.folder=getwd())

}