Package: spatialFDA 1.5.2

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:Martin Emons [aut, cre], Samuel Gunz [aut], Fabian Scheipl [aut], Elizabeth Purdom [aut], Mark D. Robinson [aut, fnd]

spatialFDA_1.5.2.tar.gz
spatialFDA_1.5.2.zip(r-4.7-any)spatialFDA_1.5.2.zip(r-4.6-any)spatialFDA_1.5.2.zip(r-4.5-any)
spatialFDA_1.5.2.tgz(r-4.6-any)spatialFDA_1.5.2.tgz(r-4.5-any)
spatialFDA_1.5.2.tar.gz(r-4.7-any)spatialFDA_1.5.2.tar.gz(r-4.6-any)
spatialFDA_1.5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spatialFDA/json (API)

# 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-1.5.2(bioc 3.24)spatialFDA-1.4.0(bioc 3.23)

software spatial transcriptomics

5.93 score 9 stars 1 packages 35 scripts 335 downloads 20 exports 130 dependencies

Last updated from:1b1c9d6f6d. Checks:1 NOTE, 4 ERROR, 4 WARNING, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	235
linux-devel	ERROR	1434
source / vignettes	ERROR	2983
linux-release	ERROR	1539
macos-release	WARNING	978
macos-oldrel	WARNING	1050
windows-devel	WARNING	1042
windows-release	ERROR	1679
windows-oldrel	WARNING	1352
wasm-release	OK	153

Exports:.dfToppp .extractMetric .loadExample .speToDf calcCrossMetricPerFov calcMetricPerFov crossSpatialInference extractCrossInferenceData functionalGam functionalPCA plotCrossFOV plotCrossHeatmap plotCrossMetricPerFov plotFbPlot plotFpca plotMdl plotMetricPerFov prepData rMaxHeuristic spatialInference

Dependencies:abind AnnotationDbi AnnotationHub ash askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 bitops blob boot cachem cli cluster colorspace cpp11 crayon curl DBI dbplyr DelayedArray deldir deSolve dplyr ExperimentHub farver fastmap fda fds filelock FNN gamm4 generics GenomicRanges ggplot2 glue goftest grpreg gtable hdrcde httr httr2 IRanges isoband jsonlite KEGGREST kernlab KernSmooth ks labeling lattice lifecycle lme4 locfit magic magick magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mgcv mime minqa multicool mvtnorm nlme nloptr openssl patchwork pbs pcaPP pillar pkgconfig png polyclip pracma purrr R6 rainbow rappdirs rbibutils RColorBrewer Rcpp RcppEigen RCurl Rdpack reformulas refund rjson rlang RLRsim RSQLite S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment sys tensor tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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
Coef for functionalGam object	coef.functionalGam
Function for Cross Spatial Inference	crossSpatialInference
Reshaping the Result of a Cross Spatial Inference to a Dataframe	extractCrossInferenceData
General additive model with functional response	functionalGam
Functional Principal Component Analysis	functionalPCA
Creates a nXn plot of the cross metrics per sample	plotCrossFOV
Plotting the Result of a Cross Spatial Inference	plotCrossHeatmap
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
Heuristic for the choice of rMax	rMaxHeuristic
Statistical Inference on Spatial Statistics Functions	spatialInference
Summary for functionalGam object	summary.functionalGam

Package: spatialFDA 1.5.2

spatialFDA: A Tool for Spatial Multi-sample Comparisons

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