Package 'multipointR'

Title: A package to compare intensities of point patterns across samples with spatial parametric models
Description: `multipointR` is a package to compare the distribution of cells in an image or cross images with point process models. On a single image level point process models (`ppm`) model the spatial distribution of a cell type point pattern as a function of spatial covariates while accounting for natural spacing of cells. The main model class considered in `multipointR` are inhomgoeneous Gibb's point process models. Across multiple images, users can either compare multiple univariate `ppm` models in a for loop or fit one joint model across all images with `mppm`. `multipointR` provides an interface between `SpatialExperiment` and `SpatialFeatureExperiment` objects and let's users flexibly define their own `ppm`/`mppm` models with R's formula interface.
Authors: Martin Emons [aut, cre] (ORCID: <https://orcid.org/0009-0000-5219-5311>), Wolfgang Huber [aut] (ORCID: <https://orcid.org/0000-0002-0474-2218>), Mark D. Robinson [aut, fnd] (ORCID: <https://orcid.org/0000-0002-3048-5518>)
Maintainer: Martin Emons <[email protected]>
License: GPL (>= 3)
Version: 0.99.6
Built: 2026-09-25 12:12:00 UTC
Source: https://github.com/bioc/multipointR

Help Index

Convert SpatialExperiment object to ppp object

Description

Convert SpatialExperiment object to ppp object

Usage

.dfToppp(df, marks = NULL, continuous = FALSE, window = NULL)

Arguments

df

DataFrame; x and y coordinates from the corresponding SpatialExperiment and the ColData
marks

character; the column with the labels e.g. cell types
continuous

logical; indicating whether the marks are continuous defaults to FALSE
window

owin; An observation window of the point pattern of class.

Value

ppp; object for use with spatstat functions

fit a shared univariate Models for all $n$ images simultaneously

Description

fit a shared univariate Models for all $n$ images simultaneously

Usage

.fitSharedModelAcrossImages(
  spe,
  model = "ppm",
  imageId,
  imageLs = NULL,
  marks,
  formula,
  family = spatstat.model::dppGauss(),
  threshold = NULL,
  interaction = "Fiksel",
  cellspacing = NA,
  lambda = NULL,
  ncores = 1,
  verbose = TRUE,
  ...
)

Arguments

spe

SpatialExperiment; object subset to a single image
model

character; the spatstat.model function to use for computation. Typically one of ppm, kppm or dppm.
imageId

character; column in the colData of the SpatialExperiment object specifying the image ID
imageLs

list; a list specifying the subset of all images. If NULL then all images are considered
marks

character; the column with the labels e.g. cell types
formula

formula; the formula to pass to the ppm function
family

detpointprocfamily; Family to use in the point process model. One of dppGauss, dppMatern, dppCauchy, dppBessel or dppPowerExp
threshold

numeric; a threshold to apply on the minimum number of points a point pattern needs to have to fit a ppm model to it.
interaction

character; Formula specifying whether to fit a Hardcore, Strauss, StraussHard or Fiksel process to the data
cellspacing

numeric how much spacing should be accounted for in the Hardcore process due to the cell body. If this is not provided, the cell spacing parameter is estimated from the data
lambda

im or NULL; offset of the intensity to include in the model to account for the underlying inhomogeneity. If this is not user provided, will be estimated as inhomogeneous intensity via diggle correction
ncores

numeric; the number of cores to used for parallel processing
verbose

logical; whether to print informations on the fitting
...

other parameters passed on to mppm model from spatstat.model

Value

list⁠; result from a ⁠ppm⁠model in⁠spatstat.model'

fit $n$ univariate Models for all $n$ images

Description

fit $n$ univariate Models for all $n$ images

Usage

.fitSingelModelsPerImage(
  spe,
  model = "ppm",
  imageId,
  imageLs = NULL,
  marks,
  formula,
  family = spatstat.model::dppGauss(),
  threshold = NULL,
  interaction = "StraussHard",
  cellspacing = NA,
  lambda = NULL,
  ncores = 1,
  verbose = TRUE,
  ...
)

Arguments

spe

SpatialExperiment; object subset to a single image
model

character; the spatstat.model function to use for computation. Typically one of ppm, kppm or dppm.
imageId

character; column in the colData of the SpatialExperiment object specifying the image ID
imageLs

list; a list specifying the subset of all images. If NULL then all images are considered
marks

character; the column with the labels e.g. cell types
formula

formula; the formula to pass to the ppm function
family

detpointprocfamily; Family to use in the point process model. One of dppGauss, dppMatern, dppCauchy, dppBessel or dppPowerExp
threshold

numeric; a threshold to apply on the minimum number of points a point pattern needs to have to fit a ppm model to it.
interaction

character; Formula specifying whether to fit a Hardcore, Strauss, StraussHard or Fiksel process to the data
cellspacing

numeric how much spacing should be accounted for in the Hardcore process due to the cell body. If this is not provided, the cell spacing parameter is estimated from the data
lambda

im or NULL; offset of the intensity to include in the model to account for the underlying inhomogeneity. If this is not user provided, will be estimated as inhomogeneous intensity via diggle correction
ncores

numeric; the number of cores to used for parallel processing
verbose

logical; whether to print informations on the fitting
...

other parameters passed on to dppm model from spatstat.model

Value

mppm object of the shared fit across all images

Transform a SpatialExperiment into a dataframe

Description

Transform a SpatialExperiment into a dataframe

Usage

.speToDf(spe)

Arguments

spe

SpatialExperiment; object subset to a single image

Value

DataFrame; x and y coordinates from the corresponding SpatialExperiment and the colData

define the Interaction Model

Description

define the Interaction Model

Usage

defineInteractionModel(interaction, cellspacing, response, data)

Arguments

interaction

character; Formula specifying whether to fit a Hardcore, Strauss, Fiksel or StraussHard process to the data
cellspacing

numeric how much spacing should be accounted for in the interaction process due to the cell body. If this is not provided, the cell spacing parameter is estimated from the data as the minimum nearest neighbour distance divided by $n(n+1)$ as done in spatstat.model::Hardcore. In the case of StraussHard, only the Strauss interaction radius can be user-provided, the Hardcore interaction is always estimated from the data.
response

character; the response for the process, the lhs of the formula object
data

list the interaction model for the Gibbs process

Value

object of class interact

Examples

spe <- SpatialDatasets::spe_Keren_2018()
speSub <- subset(spe, , imageID == "5")
formula <- as.formula("Keratin_Tumour ~ spatstat.geom::distfun(CD8_T_cell)")
# define the response
response <- as.character(formula.tools::lhs(formula))

# deparse the Formula and extract the data
out <- deparseFormula(
    spe = speSub,
    response = response,
    formula = formula,
    marks = "cellType",
    lambda = NULL,
    threshold = 10
)

interactionModel <- defineInteractionModel(
    interaction = "Hardcore",
    cellspacing = NA,
    response = response,
    data = out[["data"]]
)

deparse the Formula for spatstat and extract the relevant data

Description

deparse the Formula for spatstat and extract the relevant data

Usage

deparseFormula(spe, formula, response, marks, lambda, threshold)

Arguments

spe

SpatialExperiment; object subset to a single image
formula

formula; the formula to pass to the ppm function
response

character; the response for the process, the lhs of the formula object
marks

character; the column with the labels e.g. cell types
lambda

im or NULL; offset of the intensity to include in the model to account for the underlying inhomogeneity. If this is not user provided, will be estimated as inhomogeneous intensity via diggle correction
threshold

numeric; a threshold to apply on the minimum number of points a point pattern needs to have to fit a ppm model to it.

Value

named list with both the updated formula and the data for fitting

Examples

spe <- SpatialDatasets::spe_Keren_2018()
speSub <- subset(spe, , imageID == "5")
formula <- stats::as.formula(
    "Keratin_Tumour ~ spatstat.geom::distfun(CD8_T_cell)"
)
# define the response
response <- as.character(formula.tools::lhs(formula))

# deparse the Formula and extract the data
out <- deparseFormula(
    spe = speSub,
    response = response,
    formula = formula,
    marks = "cellType",
    lambda = NULL,
    threshold = 10
)

Fit point process models to one FOV of a SpatialExperiment object

Description

Fit point process models to one FOV of a SpatialExperiment object

Usage

fitModel(
  spe,
  model = "ppm",
  marks,
  formula,
  family = spatstat.model::dppGauss(),
  threshold = NULL,
  interaction = "Fiksel",
  lambda = NULL,
  cellspacing = NA,
  improve.type = NULL,
  relaxed = FALSE,
  ...
)

Arguments

spe

SpatialExperiment; object subset to a single image
model

character; the spatstat.model function to use for computation. Typically one of ppm, kppm or dppm.
marks

character; the column with the labels e.g. cell types
formula

formula; the formula to pass to the ppm function
family

detpointprocfamily; Family to use in the point process model. One of dppGauss, dppMatern, dppCauchy, dppBessel or dppPowerExp
threshold

numeric; a threshold to apply on the minimum number of points a point pattern needs to have to fit a ppm model to it.
interaction

character; Formula specifying whether to fit a Hardcore, Strauss, Fiksel or StraussHard process to the data
lambda

im or NULL; offset of the intensity to include in the model to account for the underlying inhomogeneity. If this is not user provided, will be estimated as inhomogeneous intensity via diggle correction
cellspacing

numeric how much spacing should be accounted for in the interaction process due to the cell body. If this is not provided, the cell spacing parameter is estimated from the data as the minimum nearest neighbour distance divided by $n(n+1)$ as done in spatstat.model::Hardcore. In the case of StraussHard, only the Strauss interaction radius can be user-provided, the Hardcore interaction is always estimated from the data.
improve.type

character the improve.type argument from spatstat.model::ppm.ppp, passed on directly
relaxed

logical whether or not to perform a relaxed fit with only the non zero coefficients from glmnet improvement
...

other parameters passed on to ppm model from spatstat.model

Value

list; result from a dppm model in spatstat.model

Examples

spe <- SpatialDatasets::spe_Keren_2018()
speSub <- subset(spe, , imageID == "5")

mdl <- fitModel(
    spe = speSub,
    marks = "cellType",
    formula = as.formula(
        "Keratin_Tumour ~ spatstat.geom::distfun(CD8_T_cell)"
    )
)

Fit point process models across all images in the SpatialExperiment object

Description

Fit point process models across all images in the SpatialExperiment object

Usage

fitModelAcrossImages(
  spe,
  model = "ppm",
  imageId,
  imageLs = NULL,
  marks,
  formula,
  family = spatstat.model::dppGauss(),
  threshold = NULL,
  interaction = "Fiksel",
  cellspacing = NA,
  lambda = NULL,
  sharedModel = FALSE,
  ncores = 1,
  verbose = TRUE,
  ...
)

Arguments

spe

SpatialExperiment; object subset to a single image
model

character; the spatstat.model function to use for computation. Typically one of ppm, kppm or dppm.
imageId

character; column in the colData of the SpatialExperiment object specifying the image ID
imageLs

list; a list specifying the subset of all images. If NULL then all images are considered
marks

character; the column with the labels e.g. cell types
formula

formula; the formula to pass to the ppm function
family

detpointprocfamily; Family to use in the point process model. One of dppGauss, dppMatern, dppCauchy, dppBessel or dppPowerExp
threshold

numeric; a threshold to apply on the minimum number of points a point pattern needs to have to fit a ppm model to it.
interaction

character; Formula specifying whether to fit a Hardcore, Strauss, StraussHard or Fiksel process to the data
cellspacing

numeric how much spacing should be accounted for in the Hardcore process due to the cell body. If this is not provided, the cell spacing parameter is estimated from the data
lambda

im or NULL; offset of the intensity to include in the model to account for the underlying inhomogeneity. If this is not user provided, will be estimated as inhomogeneous intensity via diggle correction
sharedModel

logical; whether or not to fit one univariate model per image ($n$ models in total) or estimate one shared univariate model across all images.
ncores

numeric; the number of cores to used for parallel processing
verbose

logical; whether to print informations on the fitting
...

other parameters passed on to dppm model from spatstat.model

Value

list; result from a ppm model in spatstat.model or a mppm model

Examples

spe <- SpatialDatasets::spe_Keren_2018()

mdl <- fitModelAcrossImages(
    spe = spe,
    imageId = "imageID",
    imageLs = list("1", "2"),
    marks = "cellType",
    formula = as.formula(
        "Keratin_Tumour ~ spatstat.geom::distfun(CD8_T_cell)"
    ),
    threshold = 10
)

Title

Description

Title

Usage

get_fun_call(expr, var)

Arguments

expr

part of a formula object
var

variable to extract

Value

the extracted formula call of the bespoke variable

Function to obtain the innermost call of a formula expression

Description

Function to obtain the innermost call of a formula expression

Usage

get_innermost_call(term)

Arguments

term

the term of the function to de-nest

Value

the innermost call of a nested funciton

Convert the list of spatial models to a dataframe

Description

Convert the list of spatial models to a dataframe

Usage

mdlToDf(mdlLs, imageCovariates = c("imageID"), fine = FALSE)

Arguments

mdlLs

list; A list of all the models fit with e.g. ppm
imageCovariates

list; A list of all the covariates on the image level to add to the model dataframe
fine

logical Logical flag passed to summary.ppm controlling the coarse or finer estimate of the covariance matrix

Value

DataFrame of the model coefficients

Examples

spe <- SpatialDatasets::spe_Keren_2018()

mdlLs <- fitModelAcrossImages(
    spe = spe,
    imageId = "imageID",
    imageLs = list("1", "2"),
    marks = "cellType",
    sharedModel = FALSE,
    formula = as.formula(
        "Keratin_Tumour ~ spatstat.geom::distfun(CD8_T_cell)"
    ),
    threshold = 10
)

mdlDf <- mdlToDf(
    mdlLs = mdlLs,
    imageCovariates = c(
        "imageID",
        "tumour_type"
    )
)

Plot mulitpointR ppm objects

Description

Plot mulitpointR ppm objects

Usage

## S3 method for class 'multipointRppm'
plot(x, type = "trend", ...)

Arguments

x

ppm; a model fit with spatstat.model::ppm or the wrapper multipointR::fitModel
type

character; the type to plot, one of "intensity" or "trend"
...

further arguments passed to geom_raster

Value

a ggplot2 object of the model trend/intensity surfance

Examples

spe <- SpatialDatasets::spe_Keren_2018()
speSub <- subset(spe, , imageID == "5")

mdl <- fitModel(
    spe = speSub,
    marks = "cellType",
    formula = as.formula(
        "Keratin_Tumour ~ spatstat.geom::distfun(CD8_T_cell)"
    )
)
plot(mdl)

convert a SpatialExperiment object into a point pattern

Description

convert a SpatialExperiment object into a point pattern

Usage

speToPPP(spe, marks, continuous = FALSE, window = NULL)

Arguments

spe

SpatialExperiment; object subset to a single image
marks

character; the column with the labels e.g. cell types
continuous

logical; indicating whether the marks are continuous defaults to FALSE
window

owin; An observation window of the point pattern of class.

Value

A ppp object for use with any spatstat package

Examples

spe <- SpatialDatasets::spe_Keren_2018()
speSub <- subset(spe, , imageID == "6")
pp <- speToPPP(speSub, mark = "cellType")