tests/testthat/test_pcagenes.R

In pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach

library(pcaExplorer)

context("Checks on the pca on the genes")

library(DESeq2)
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- rlogTransformation(dds)

groups <- colData(dds)$condition
cols <- scales::hue_pal()(2)[groups]
genespca(rlt, ntop = 100, arrowColors = cols, groupNames = groups)
dat <- genespca(rlt, ntop = 100, arrowColors = cols, groupNames = groups, returnData = TRUE)


genespca(rlt, ntop = 100)

genespca(rlt, ntop = 100, arrowColors = "green")

expect_error(genespca(rlt, ntop = 100, arrowColors = c("green", "red")))

groups_multi <- interaction(as.data.frame(colData(rlt)[, c("condition", "tissue")]))
cols_multi <- scales::hue_pal()(length(levels(groups_multi)))[factor(groups_multi)]
genespca(rlt, ntop = 100, arrowColors = cols_multi, groupNames = groups_multi)