makepHeatmap: plots a heatmap

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

plots a heatmap

Description

plots a heatmap

Usage

makepHeatmap(
  mx,
  nCol = 200,
  col = "default",
  maxVal = "default",
  minVal = "default",
  label = "",
  DEsaturation = log2(10),
  reverseGradient = F,
  border_color = NA,
  cluster_rows = F,
  cluster_cols = F,
  ...
)

Arguments

mx	numeric. The matrix to be plotted.
nCol	numeric. The number of colours in the gradient. Default 200.
col	character. The colour scheme to be used. The default 'default' gives a scale adapted for freqwuencies between 0 and 1, with extra attention to values close to 0. 'sunset' is a easier on the eye, but has less ability to resolve values close to the lowest value. 'DE' is meant for differential expression, and sets 0 to black, with red and blue gradient towards positive and negative values, saturating at the DEsaturation parameter.
maxVal	numeric. Only for internal use. Default 'default'.
minVal	numeric. Only for internal use. Default 'default'.
label	character. The label for the colour scale on the side. Default ”.
DEsaturation	numeric. The value where the colour saturates when col='DE'. Default log2(10).
...	remaining arguments are passed to base heatmap(...)

Details

This function is a wrapped pheatmap() function with some changed colours and defaults. Depends on pheatmap package, which is not a superFreq dependency, so need to load that library before using this.

Examples

#random matrix to plot, centered around 0. Plot in 'DE' colours.
mx = matrix(rt(400, df=10), nrow=100)
makeHeatmap(mx, col='DE')

#random matrix to plot, between 0 and 1. Plot in default and sunset colours.
mx = matrix(runif(400), nrow=100)
makeHeatmap(mx)
makeHeatmap(mx, col='sunset')

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.