plotImg: Plot raster images of type 'im'

In CeMOS-Mannheim/moleculaR: Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging

Plot raster images of type 'im'

Description

A method to plot 'im' objects of the 'spatstat' package. This calls 'plot.im' with pre-defined defaults. For more control over the plotting please use 'plot.im'.

Usage

plotImg(
  obj,
  colourPal = "inferno",
  uniformCol = NULL,
  rescale = TRUE,
  smooth = FALSE,
  transpFactor = 1,
  irange = NULL,
  ribargs = list(las = 2, cex.axis = 1.25),
  ribsep = 0.05,
  ...
)

Arguments

obj	S3 object of type 'im'.
colourPal	the colourmap to be used, see '?viridis::viridis_pal'.
uniformCol	a character specifying a single colour. This will override 'colourPal'.
rescale	logical, whether to scale the intensities of the output plot to (0,1] interval.
smooth	logical, whether to apply image smoothing via an isotropic Gaussian kernel.
transpFactor	Transparency fraction. Numerical value or vector of values between 0 and 1, giving the opaqueness of a colour. A fully opaque colour has 'transpFactor=1'.
irange	a numeric of length 2, a custome intensity range for plotting. Incompatible with 'rescale'; if provided, 'rescale' will be set to 'FALSE'.
ribargs	a list of additional arguments to control the display of the ribbon. see '?spatstat.geom::plot.im' for details.
ribsep	a numeric controlling the space between the ribbon and the image.
...	further arguments passed to 'plot.im'.

Value

nothing, plots only.

CeMOS-Mannheim/moleculaR documentation built on April 14, 2025, 8:27 a.m.