hi_loadings {pcaExplorer} | R Documentation |
Extract genes with highest loadings
hi_loadings(pcaobj, whichpc = 1, topN = 10, exprTable = NULL, annotation = NULL, title = "Top/bottom loadings")
pcaobj |
A |
whichpc |
An integer number, corresponding to the principal component of interest |
topN |
Integer, number of genes with top and bottom loadings |
exprTable |
A |
annotation |
A |
title |
The title of the plot |
A ggplot2 object, or a matrix
, if exprTable
is not null
dds <- makeExampleDESeqDataSet_multifac(betaSD = 3,betaSD_tissue = 1) rlt <- DESeq2::rlogTransformation(dds) pcaobj <- prcomp(t(SummarizedExperiment::assay(rlt))) hi_loadings(pcaobj, topN = 20) hi_loadings(pcaobj, topN = 10, exprTable=dds) hi_loadings(pcaobj, topN = 10, exprTable=counts(dds))