Log2-transform an assay matrix and subset/order it to the requested genes

Zeros are mapped to log2(1) = 0 rather than dropped to NA (the default rmzeros = FALSE): unlike a per-sample boxplot, where dropping a handful of zero values out of thousands of genes is harmless, a gene can legitimately be all-zero in one whole condition - exactly the genes an absolute-fold-change ranking surfaces - and dropping those to NA would erase that side's box entirely instead of showing it pinned at zero.

Usage

topgeneTransformAssay(assay, genes, should_transform = NULL)

Arguments

assay

Numeric matrix, genes (rows) by samples (columns)

genes

Character vector of row names of assay to facet on, in the order facets should appear. Also used to look up values in assay, so must match its row names even when labels is supplied.

should_transform

A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.

Value

The transformed matrix, subset to genes in that order