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