Package: spatialFDA 0.99.12
Martin Emons
spatialFDA: A Tool for Spatial Multi-sample Comparisons
spatialFDA is a package to calculate spatial statistics metrics. The package takes a SpatialExperiment object and calculates spatial statistics metrics using the package spatstat. Then it compares the resulting functions across samples/conditions using functional additive models as implemented in the package refund. Furthermore, it provides exploratory visualisations using functional principal component analysis, as well implemented in refund.
Authors:
spatialFDA_0.99.12.tar.gz
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spatialFDA.pdf |spatialFDA.html✨
spatialFDA/json (API)
NEWS
| # Install 'spatialFDA' in R: |
| install.packages('spatialFDA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mjemons/spatialfda/issues
On BioConductor:spatialFDA-0.99.11(bioc 3.21)
softwarespatialtranscriptomics
Last updated 20 days agofrom:19a8193e15. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 20 2025 |
| R-4.5-win | OK | Feb 20 2025 |
| R-4.5-mac | OK | Feb 20 2025 |
| R-4.5-linux | OK | Feb 20 2025 |
| R-4.4-win | OK | Feb 20 2025 |
| R-4.4-mac | OK | Feb 20 2025 |
| R-4.3-win | OK | Feb 20 2025 |
| R-4.3-mac | OK | Feb 20 2025 |
Exports:.dfToppp.extractMetric.loadExample.speToDfcalcCrossMetricPerFovcalcMetricPerFovfunctionalGamfunctionalPCAplotCrossFOVplotCrossMetricPerFovplotFbPlotplotFpcaplotMdlplotMetricPerFovprepData
Dependencies:abindAnnotationDbiAnnotationHubashaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64bitopsblobbootcachemcliclustercolorspacecpp11crayoncurlDBIdbplyrDelayedArraydeldirdeSolvedplyrExperimentHubfansifarverfastmapfdafdsfilelockFNNgamm4genericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegoftestgrpreggtablehdrcdehttrIRangesisobandjsonliteKEGGRESTkernlabKernSmoothkslabelinglatticelifecyclelme4locfitmagicmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminqamulticoolmunsellmvtnormnlmenloptropensslpatchworkpbspcaPPpillarpkgconfigplogrpngpolyclippracmapurrrR6rainbowrappdirsrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasrefundrjsonrlangRLRsimRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert SpatialExperiment object to ppp object | .dfToppp |
| Compute a spatial metric on a SpatialExperiment object | .extractMetric |
| load Example dataset from Damond et al. (2019) | .loadExample |
| Transform a SpatialExperiment into a dataframe | .speToDf |
| Calculate cross spatial metrics for all combinations per FOV | calcCrossMetricPerFov |
| Calculate a spatial metric on a 'SpatialExperiment' object per field of view | calcMetricPerFov |
| General additive model with functional response | functionalGam |
| Functional Principal Component Analysis | functionalPCA |
| Creates a nXn plot of the cross metrics per sample | plotCrossFOV |
| Plot a cross type spatial metric per field of view | plotCrossMetricPerFov |
| Functional boxplot of spatstat curves | plotFbPlot |
| Plot a biplot from an fPCA analysis | plotFpca |
| Plot a pffr model object | plotMdl |
| Plot a spatial metric per field of view | plotMetricPerFov |
| Prepare data from calcMetricRes to be in the right format for FDA | prepData |
| print the fPCA results | print.fpca |
