Package: multipointR 0.99.0
multipointR: A package to compare intensities of point patterns across samples with spatial parametric models
`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:
multipointR_0.99.0.tar.gz
multipointR_0.99.0.zip(r-4.7)multipointR_0.99.0.zip(r-4.6)multipointR_0.99.0.zip(r-4.5)
multipointR_0.99.0.tgz(r-4.6-any)multipointR_0.99.0.tgz(r-4.5-any)
multipointR_0.99.0.tar.gz(r-4.7-any)multipointR_0.99.0.tar.gz(r-4.6-any)
multipointR_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
multipointR/json (API)
| # Install 'multipointR' in R: |
| install.packages('multipointR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biocstaging/multipointr/issues
softwarespatialtranscriptomics
Last updated from:f9a3e7ab9d. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 243 | ||
| linux-devel-x86_64 | OK | 572 | ||
| source / vignettes | OK | 660 | ||
| linux-release-x86_64 | OK | 569 | ||
| macos-release-arm64 | OK | 459 | ||
| macos-oldrel-arm64 | OK | 367 | ||
| windows-devel | OK | 691 | ||
| windows-release | OK | 652 | ||
| windows-oldrel | OK | 636 | ||
| wasm-release | OK | 201 |
Exports:.dfToppp.fitSharedModelAcrossImages.fitSingelModelsPerImage.speToDfdefineInteractionModeldeparseFormulafitModelfitModelAcrossImagesmdlToDfspeToPPP
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydeldirdplyrfarverfastmapfilelockformula.toolsgenericsGenomicRangesggplot2gluegoftestgtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvnlmeopenssloperator.toolspillarpkgconfigpolyclippurrrR6rappdirsrbibutilsRColorBrewerRcppRdpackreformulasrjsonrlangrpartRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert SpatialExperiment object to ppp object | .dfToppp |
| fit a shared univariate Models for all $n$ images simultaneously | .fitSharedModelAcrossImages |
| fit $n$ univariate Models for all $n$ images | .fitSingelModelsPerImage |
| Transform a SpatialExperiment into a dataframe | .speToDf |
| define the Interaction Model | defineInteractionModel |
| deparse the Formula for spatstat and extract the relevant data | deparseFormula |
| Fit point process models to one FOV of a 'SpatialExperiment' object | fitModel |
| Fit point process models across all images in the 'SpatialExperiment' object | fitModelAcrossImages |
| Convert the list of spatial models to a dataframe | mdlToDf |
| Plot mulitpointR 'ppm' objects | plot.multipointRppm |
| convert a SpatialExperiment object into a point pattern | speToPPP |
