plotZmap: Plots a Z-map

In rdotsch/rcicr: Reverse-Correlation Image-Classification Toolbox

Plots a Z-map

Description

Plots a Z-map given a matrix of z-scores that maps onto a specified base image.

Usage

plotZmap(
  zmap,
  bgimage = "",
  sigma,
  threshold = 3,
  mask = NULL,
  decoration = T,
  targetpath = "zmaps",
  filename = "zmap",
  size = 512,
  ...
)

Arguments

zmap	A matrix containing z-scores that map onto a given base image. zmap and baseimage must have the same dimensions.
bgimage	A matrix containing the grayscale image to use as a background. This should be either the base image or the final CI. If not this argument is not given, only the Z-map will be drawn.
sigma	The sigma of the smoothing that was applied to the CI to create the Z-map.
threshold	Integer specifying the threshold z-score (default: 3). Z-scores below the threshold will not be plotted on the z-map.
mask	Optional. A boolean matrix with the same dimensions as zmap. If a cell evaluates to TRUE, the corresponding zmap pixel will be masked. Can also be the filename (as a string) of a black and white PNG image to be converted to a matrix (black = masked).
decoration	Optional boolean specifying whether the Z-map should be plotted with margins, text (sigma, threshold) and a scale (default: TRUE).
targetpath	String specifying path to save the Z-map PNG to.
filename	Optional string to specify a file name for the Z-map PNG.
size	Integer specifying the width and height of the PNG image (default: 512).
...	Additional arguments to be passed to raster::plot. Only applied when decoration is TRUE.

Details

This function takes in a matrix of z-scores (as returned by generateCI) and an Rdata file containing a base image. It returns a Z-map image in PNG format. Unlisted additional arguments will be passed to raster::plot. For example, a different color palette can be specified using the col argument. See raster::plot for details.

Value

Nothing. It writes a Z-map image.

rdotsch/rcicr documentation built on Feb. 5, 2023, 10:15 p.m.