Basics | Installing spaSim | Citing spaSim | Quick start to using spaSim | Simulate an individual image | Simulate background cells | Simulate mixed background | Simulate clusters | Simulate immune rings | Simulate double rings | Simulate vessels | Displaying the sequential construction of a simulated image | Simulating a range of multiple images | Simulate multiple background images (multiple cell types) with different proportions of cell types. | Simulate multiple images with clusters of different properties. | Simulate multiple images with immune rings of different properties | Input simulated images into r Biocpkg("SPIAT") package. | Citation | Reproducibility | Bibliography
Package: spaSim 1.15.0
Yuzhou Feng
spaSim: Spatial point data simulator for tissue images
A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.
Authors:
spaSim_1.15.0.tar.gz
spaSim_1.15.0.zip(r-4.7)spaSim_1.15.0.zip(r-4.6)spaSim_1.15.0.zip(r-4.5)
spaSim_1.15.0.tgz(r-4.6-any)spaSim_1.15.0.tgz(r-4.5-any)
spaSim_1.15.0.tar.gz(r-4.7-any)spaSim_1.15.0.tar.gz(r-4.6-any)
spaSim_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spaSim/json (API)
| # Install 'spaSim' in R: |
| install.packages('spaSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/trigosteam/spasim/issues
Pkgdown/docs site:https://trigosteam.github.io
Datasets:
- bg1 - Background cells
On BioConductor:spaSim-1.15.0(bioc 3.24)spaSim-1.14.0(bioc 3.23)
statisticalmethodspatialbiomedicalinformatics
Last updated from:2cc39a7394. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 192 | ||
| linux-devel-x86_64 | NOTE | 433 | ||
| source / vignettes | OK | 348 | ||
| linux-release-x86_64 | NOTE | 429 | ||
| macos-release-arm64 | NOTE | 226 | ||
| macos-oldrel-arm64 | NOTE | 250 | ||
| windows-devel | NOTE | 350 | ||
| windows-release | NOTE | 365 | ||
| windows-oldrel | NOTE | 319 | ||
| wasm-release | OK | 144 |
Exports:multiple_background_imagesmultiple_images_with_clustersmultiple_images_with_immune_ringssimulate_background_cellssimulate_clusterssimulate_double_ringssimulate_immune_ringssimulate_mixingsimulate_stripesTIS
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydeldirdplyrfarverfastmapfilelockgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpolyclippurrrR6RANNrappdirsRColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentspatstat.dataspatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Background cells (4915 cells in a 2000*2000 window) | bg1 |
| format_spe | format_spe |
| Simulate multiple background images (mixed cell types) | multiple_background_images |
| Simulate multiple images with clusters | multiple_images_with_clusters |
| Simulate multiple images with immune rings | multiple_images_with_immune_rings |
| plot_cells | plot_cells |
| Simulate background cells | simulate_background_cells |
| Simulate clusters | simulate_clusters |
| Simulate double immune rings | simulate_double_rings |
| simulate_immune_rings | simulate_immune_rings |
| Simulate mixed background image | simulate_mixing |
| simulate_stripes | simulate_stripes |
| Tissue Image Simulator (TIS) | TIS |