plotAnalyte: Plot analytePointPattern

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

Plot analytePointPattern

Description

A method to plot 'anlaytePointPattern' objects. This calls 'plot.ppp' with pre-defined defaults. For more control over the plotting please use 'plot.ppp'.

Usage

plotAnalyte(
  obj,
  colourPal = "inferno",
  uniformCol = NULL,
  transpFactor = 1,
  rescale = TRUE,
  pch = 19,
  size = 0.4,
  main = NULL,
  leg.side = "right",
  leg.args = list(cex = 3, cex.axis = 1.25),
  ...
)

Arguments

obj	S3 object of type 'anlaytePointPattern' (and 'spp').
colourPal	the colourmap to be used, see '?viridis::viridis_pal'.
uniformCol	a character specifying a single colour. This will override 'colourPal'.
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'.
rescale	logical, whether to scale the intensities of the output plot to [0,1] interval.
pch	a positive integer, or a single character. See '?par'.
size	the size of the symbol: a positive number or zero. see'?symbolmap'.
main	character, title of the plot. If not given, the m/z value of 'obj' is used.
leg.side	position of legend relative to main plot.
leg.args	list of additional arguments passed to control the legend. see '?spatstat.geom::plot.ppp' for more details.
...	further arguments passed to 'spatstat.geom::plot.ppp'.

Value

nothing, plots only.

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