HeatmapCNR: HeatmapCNR

In SingerLab/gac: Genetic Analysis of Cells

HeatmapCNR

Description

Wrapper function to the ultra-powerful ComplexHeatmap. It implements Bray-Curtis dissimilarity as the distance metric for clustering cells, and 'ward.D2' from 'hclust'. Bray-Curtis disimilarity is extensively used in Ecology for clustering comunities.

Usage

HeatmapCNR(
  cnr,
  what = "X",
  which.genes = NULL,
  col = NULL,
  base.ploidy = 2,
  show_row_dend = FALSE,
  ...
)

Arguments

cnr	the CNR bundle
what	wether you want to plot bins or genes
which.genes	IF you chose genes, you need to specify which ones
col	optional color map, if NULL colors are dependent on the sample ploidy: For base.ploidy = 2; values are 0 = yellow, 1 = blue, 2 = white, 3-10 reds, >10 greyscale For base.ploidy = 4; values are a <4 = dark to light blues, 4 = yellow, >4 = light to dark reds if cnr$bulk = TRUE, ratios are blue, white, and red.
base.ploidy	base ploidy, values must be 2 or 4. Defaults to 2. Ignored if setting color pallete
show_row_dend	weather to show the row dendrogram, default is FALSE,
...	additional parameters from Heatmap

Details

If you prefer to use a different method, you can use the native Heatmap function. E.g. if you prefer genomic bins to cluster, and show a dendrogram when plotting X. By default bins are kept in chromosome order, however, when plotting genes, rows are cells, and these are clustered.

Value

Returns a simple ComplexHeatmap plot clustered using Bray-Disimilarity with vegan::vegdist, and sorted by chromosome location.

For custumizing your heatmap, please visit the ComplexHeatmap documentation:

https://jokergoo.github.io/ComplexHeatmap-reference/book/

Examples

## load example
data(cnr)

HeatmapCNR(cnr)

HeatmapCNR(cnr, what = "genes", which.genes = c("CDK4", "MDM2"))

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.