imageWithScale: Plot a matrix as a heatmap in its natural orientation, with a...

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Plot a matrix as a heatmap in its natural orientation, with a colored scale on the right side, and optionally using its dimension names for rows and columns

Description

To print all row names, choose idx.rownames=1:nrow(z). To print a subset of 10 row names, choose idx.rownames=floor(seq(1, nrow(z), length.out=10)). Similarly for column names.

Usage

imageWithScale(
  z,
  main = NULL,
  idx.rownames = NULL,
  idx.colnames = NULL,
  breaks = NULL,
  nb.breaks = 20,
  left.text.at = NULL,
  cex.txt = 1,
  cex.sc = 1,
  col.pal = grDevices::colorRampPalette(c("black", "red", "yellow"), space = "rgb"),
  custom.mar = NULL
)

Arguments

z	matrix to be plotted
main	title to appear above the heatmap
idx.rownames	vector giving the indices of the row names of z to be added on the left side of the plot
idx.colnames	vector giving the indices of the column names of z to be added on top of the plot
breaks	vector of breaks (if NULL, will be seq(min(z), max(z), length.out=nb.breaks))
nb.breaks	number of breaks
left.text.at	vector which names and values will be used to label the left side of the plot; if not NULL, takes precedence over idx.rownames
cex.txt	numeric character expansion factor used with "left.text.at"
cex.sc	numeric character expansion factor used with the scale
col.pal	output of colorRampPalette
custom.mar	see par

Author(s)

Timothee Flutre

Examples

## Not run: set.seed(1859)
genomes <- simulCoalescent(nb.inds=200, nb.pops=3, mig.rate=3)
X <- genomes$genos
A <- estimGenRel(X=X, relationships="additive", method="vanraden1")
imageWithScale(z=A, main="Additive genetic relationships", breaks=seq(0,1,length.out=20),
               left.text.at=setNames(c(0.83, 0.5, 0.17), c("pop1", "pop2", "pop3")))

## End(Not run)

timflutre/rutilstimflutre documentation built on Aug. 18, 2024, 7:43 p.m.