Package: scSpatialSIM 0.1.3.4
Fridley Lab
scSpatialSIM: A Point Pattern Simulator for Spatial Cellular Data
Single cell resolution data has been valuable in learning about tissue microenvironments and interactions between cells or spots. This package allows for the simulation of this level of data, be it single cell or ‘spots’, in both a univariate (single metric or cell type) and bivariate (2 or more metrics or cell types) ways. As more technologies come to marker, more methods will be developed to derive spatial metrics from the data which will require a way to benchmark methods against each other. Additionally, as the field currently stands, there is not a gold standard method to be compared against. We set out to develop an R package that will allow users to simulate point patterns that can be biologically informed from different tissue domains, holes, and varying degrees of clustering/colocalization. The data can be exported as spatial files and a summary file (like 'HALO'). <https://github.com/FridleyLab/scSpatialSIM/>.
Authors:
scSpatialSIM_0.1.3.4.tar.gz
scSpatialSIM_0.1.3.4.zip(r-4.5)scSpatialSIM_0.1.3.4.zip(r-4.4)scSpatialSIM_0.1.3.4.zip(r-4.3)
scSpatialSIM_0.1.3.4.tgz(r-4.4-any)scSpatialSIM_0.1.3.4.tgz(r-4.3-any)
scSpatialSIM_0.1.3.4.tar.gz(r-4.5-noble)scSpatialSIM_0.1.3.4.tar.gz(r-4.4-noble)
scSpatialSIM_0.1.3.4.tgz(r-4.4-emscripten)scSpatialSIM_0.1.3.4.tgz(r-4.3-emscripten)
scSpatialSIM.pdf |scSpatialSIM.html✨
scSpatialSIM/json (API)
# Install 'scSpatialSIM' in R: |
install.packages('scSpatialSIM', repos = c('https://fridleylab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fridleylab/scspatialsim/issues
- wm - Round spatstat window
Last updated 2 months agofrom:2f236dfdea. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 18 2024 |
R-4.5-win | OK | Nov 18 2024 |
R-4.5-linux | OK | Nov 18 2024 |
R-4.4-win | OK | Nov 18 2024 |
R-4.4-mac | OK | Nov 18 2024 |
R-4.3-win | OK | Nov 18 2024 |
R-4.3-mac | OK | Nov 18 2024 |
Exports:%>%CalculateDensityCreateSimulationObjectCreateSpatialListExtractParametersGenerateCellPositivityGenerateDistributionsGenerateHolesGenerateSpatialPatternGenerateTissuePlotSimulationSummariseSpatialUpdateSimulationWindow
Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11crayondeldirDerivdoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpbmcapplypillarpkgconfigpolyclippolynomproxypurrrquantregR6RColorBrewerRcppRcppEigenrlangrstatixscalesSparseMspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilsstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Compute Simulation Heatmaps | CalculateDensity |
Create a spatial simulation object. | CreateSimulationObject |
Get Spatial Files from a 'SpatSimObj' | CreateSpatialList |
Get Simulation Parameters | ExtractParameters |
Generate Cell Positivity | GenerateCellPositivity |
Generate Characteristic Distributions of Cells | GenerateDistributions |
Generate holes in a spatial simulation object | GenerateHoles |
Generate Spatial Point Pattern | GenerateSpatialPattern |
Generate Tissue | GenerateTissue |
plot function for SpatSimObj | plot.SpatSimObj |
Plot Simulation | PlotSimulation |
Summarise Spatial | SummariseSpatial |
summary function for SpatSimObj | summary.SpatSimObj |
Update the simulation window in a SpatSimObj | UpdateSimulationWindow |
Round spatstat window | wm |