analytePointPattern: analytePointPattern Class Constructor

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

analytePointPattern Class Constructor

Description

This is a class to extend 'ppp' class only enforcing specific point-marks. It also adds a 'metaData' slot to declare which analytes are constructing a given 'analytePointPattern' object. It represents the spatial point pattern of an analyte (or set of analytes) with marks being a data.frame of two columns c('idx', 'intensity'). This constructor is for internal use and normally should not be called by the user.

Usage

analytePointPattern(
  spp = NA,
  x = NA,
  y = NA,
  win = NA,
  intensity = NA,
  mzVals,
  metaData = list()
)

Arguments

spp	a spatial point pattern of type 'ppp' with its 'marks' being a dataframe with two columns 'idx'and 'intensity'.
x, y, intensity, win	optional, either these arguments or 'spp' have to be supplied.
metaData	a named list having additional attributes describing the individual masses in 'mzVals'.

Details

'mzVals' and 'metaData' are combined into a data.frame which becomes a class slot 'metaData'. This contains the 'mzVals' and possible other meta data with each row having a unique identifier 'idx' which then link 'metaData' with 'spp$marks'.

Value

An S3 object of type 'ppp' and 'analytePointPattern' with the following entries

• regular 'ppp' entries: see 'spatstat' documentation for 'ppp' class.

• metaData: A data frame with meta data describing the points in 'spp$marks'.

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