Reshape an assay matrix into long form for static_topgene_boxplots

Reshape an assay matrix into long form for static_topgene_boxplots

Usage

topgeneBoxplotData(assay, groupby, genes, should_transform = NULL)

Arguments

assay

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

groupby

Vector of group labels, one per column of assay

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

A data frame with columns gene (factor, levels = genes), group (factor, first-seen order) and value