plotMatrix: Plot Matrix

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Plot Matrix

Description

This function plots a matrix of values. Data is visualised as circles scaled with respect to the largest value in the matrix, with the actual number shown. If thresholdMark is specified, then a different colour is used for entries that are equal or above the threshold.

Usage

plotMatrix(
  dataMatrix,
  output_file = NULL,
  thresholdMark = NULL,
  ndigitsafterzero = 2,
  cex.numbers = 0.7,
  title = NULL,
  circlesColBasic = "#A1CAF1",
  circlesColHighlight = "#F6A600",
  sideVector = NULL,
  sideVectorLabel = NULL,
  sideVectorColours = c("#cf0000", "#F38400", "#8DB600"),
  sideVectorThresholds = c(0.8, 0.9),
  sideVectorNdigitsafterzero = 2
)

Arguments

dataMatrix	a data matrix or data frame
output_file	if an output file name is given (must be pdf), the matrix will be plotted to file
thresholdMark	threshold for using a different colour to highlight entries above a threshold
ndigitsafterzero	specify how many digits after the zero should be used to show the actual numbers
cex.numbers	scale the text used for the numbers in the matrix
circlesColBasic	colour used for the circles
circlesColHighlight	colour used for the circles that pass the thresholdMark
sideVector	optional vector that should be of the same length as the number of columns of dataMatrix. Leave NULL to omit. If specified, the values will be plotted on the left, leaving a gap from the main plotted matrix and using sideVectorLabel as the label for this column, as well as the colours in sideVectorColours
sideVectorLabel	label to be used when sideVector is specified
sideVectorColours	colours to be used for the sideVector circles. This vector should be one element longer than sideVectorThresholds
sideVectorThresholds	boundaries for using the sideVectorColours according to the values of sideVector. Values need to be increasing. For example, values of sideVector lower than sideVectorThresholds[1] will be coloured sideVectorColours[1], and values greater than sideVectorThresholds[length(sideVectorThresholds)] will be coloured sideVectorColours[length(sideVectorThresholds)+1]
sideVectorNdigitsafterzero	similar to ndigitsafterzero, but only affects sideVector values

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.