plot_genes: Plot heatmap of top genes

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Plot heatmap of top genes

Description

Plot heatmap of top genes with annoation bars, reordered branches, and color scale midpoint at zero.

Usage

plot_genes(
  x,
  intgroup,
  palette = "RdBu",
  dendsort = TRUE,
  scale = "none",
  midpoint0 = TRUE,
  max_scale = NA,
  border = NA,
  cluster_cols = TRUE,
  ...
)

Arguments

x	a tibble from top_counts
intgroup	one or more column names for pheatmap annotation_col bar
palette	RColorBrewer palette name, vector of colors, or "RdGn" for Red-Green color scale.
dendsort	reorder branches using dendsort package
scale	scale values, default none. diff will substract the row mean from each value. Other options are none, row and column as described in heatmap
midpoint0	if scale = diff, then center color scale at zero
max_scale	if scale = diff, then max value for color scale, default is max(abs(range(x)))
border	pheatmap border color, default NA
cluster_cols	cluster columns
...	additional options passed to pheatmap or d3heatmap

Value

A pheatmap

Author(s)

Chris Stubben

Examples

x <- top_counts(pasilla$results, pasilla$rlog)
plot_genes(x, c("condition", "type"), scale="row", annotation_names_col=FALSE)
# plot_genes(x, output = "d3")

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