plot.molProbMap: Plot molecular Probability Maps

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

Plot molecular Probability Maps

Description

A method to plot MPMs with different combinations.

Usage

## S3 method for class 'molProbMap'
plot(
  obj,
  what = "detailed",
  densityAsBase = FALSE,
  sppArgs = list(),
  imageArgs = list(),
  fArgs = list(),
  rescale = TRUE,
  smooth = FALSE,
  zero.rm = FALSE,
  signifArea = "both",
  ionImage = NA,
  figLegend = TRUE,
  lwd.signifArea = 5,
  col.hotspot = "red",
  col.coldspot = "blue"
)

Arguments

obj	S3 object of type 'molProbMap'.
what	What to plot, c("detailed", "analytePointPattern", "csrPointPattern", "analyteDensityImage", "csrDensityImage", "kdeIntensitiesDistr", "MPM"). The "detailed" option plots all options.
densityAsBase	a logical, if set to 'TRUE', the base image, ontop of which hotspot/coldspot contours are plotted, is taken from the estimated density image of m/z MOI. Otherwise (default), the Gaussian-weighted ion image is used.
sppArgs	a named list of arguments to be passed to 'plotAnalyte' or plotting "analytePointPattern" and "csrPointPattern". There are sensible defaults.
imageArgs	a named list of arguments to be passed to 'spatstat.geom::plot.im' for plotting "analyteDensityImage", "csrDensityImage" and "MPM". There are sensible defaults.
fArgs	a named list of arguments to be passed to 'base::plot' for plotting "kdeIntensitiesDistr". There are sensible defaults.
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.
zero.rm	logical, whether to remove zero-valued pixels from the intensity image.
signifArea	a character indicating which significance area to plot i.e. c("both", "hotspot", "coldspot").
ionImage	an optional rastered image of type 'im' of the corresponding "regular" ion image, used for comparison. Could be generated via 'moleculaR::searchAnalyte(..., wMethod = "sum")' and subsequently using 'pixellate'.
figLegend	logical, whether to show the hotspot and coldspot legends.
lwd.signifArea	numeric, the width of the hotspot and coldspot contours.
col.hotspot	a character specifying the color of the hotspot contour.
col.coldspot	a character specifying the color of the coldspot contour.

Value

nothing, plots only.

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