prune_mat: Prune matrix

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Prune matrix

Description

Prune (subset) rows of matrix for plotting as heatmap.

Usage

prune_mat(
  object,
  labrows = rownames(object),
  only.labrows = FALSE,
  unique.rows = FALSE,
  ntop = NULL,
  na.lab = c("---", ""),
  verbose = TRUE
)

Arguments

object	Matrix-like object with features (e.g. genes) as rows and samples as columns.
labrows	Labels for rows, e.g. gene symbols. This can be of length 1 (in which case it is recycled), of length nrow(object).
only.labrows	Logical; only include rows where labrows aren't missing (missing is defined by na.lab)?
unique.rows	Logical; remove duplicated row labels to make rows unique?
ntop	Scalar number of rows to include.
na.lab	Character vector of labels in lab.col to treat as missing, in addition to NA.
verbose	Logical; print pruning messages to console?

Value

Vector of pruned matrix rownames; vectors names are from rownames(object).

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.