plot_dist: Plot heatmap of sample distances

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Plot heatmap of sample distances

Description

Plot sample distances using rlog or other counts.

Usage

plot_dist(
  rld,
  intgroup,
  col_name,
  palette = "RdYlBu",
  reverse_pal = FALSE,
  diagNA = TRUE,
  border = NA,
  fontsize = 10,
  ...
)

Arguments

rld	a matrix or DESeqTransform with assay slot
intgroup	one or more column names in colData(rld) for pheatmap annotation_col
col_name	Column name in 'colData(rld)' for labels, default is sample IDs in colnames(rld)
palette	a color palette name or vector of colors
reverse_pal	reverse the color palette
diagNA	set the diagonal to NA, default TRUE
border	pheatmap border color, default none
fontsize	x and yaxis font size
...	Additional options like colors passed to d3heatmap or pheatmap

Value

A pheatmap

Author(s)

Chris Stubben

Examples

plot_dist(pasilla$rlog, c("condition", "type"), na_col="white")
plot_dist(pasilla$rlog, c("condition", "type"), palette="Blues", diagNA=FALSE, reverse=TRUE)

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.