Package: spaSim 1.9.0

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:Yuzhou Feng [aut, cre], Anna Trigos [aut]

spaSim_1.9.0.tar.gz
spaSim_1.9.0.zip(r-4.5)spaSim_1.9.0.zip(r-4.4)spaSim_1.9.0.zip(r-4.3)
spaSim_1.9.0.tgz(r-4.4-any)spaSim_1.9.0.tgz(r-4.3-any)
spaSim_1.9.0.tar.gz(r-4.5-noble)spaSim_1.9.0.tar.gz(r-4.4-noble)
spaSim_1.9.0.tgz(r-4.4-emscripten)spaSim_1.9.0.tgz(r-4.3-emscripten)
spaSim.pdf |spaSim.html✨
spaSim/json (API)
NEWS

# 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

Datasets:

bg1 - Background cells

On BioConductor:spaSim-1.9.0(bioc 3.21)spaSim-1.8.0(bioc 3.20)

statisticalmethod spatial biomedicalinformatics

5.18 score 2 stars 25 scripts 128 downloads 10 exports 86 dependencies

Last updated 25 days agofrom:27c44e5bf6. Checks:OK: 3 NOTE: 1 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:multiple_background_images multiple_images_with_clusters multiple_images_with_immune_rings simulate_background_cells simulate_clusters simulate_double_rings simulate_immune_rings simulate_mixing simulate_stripes TIS

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli colorspace cpp11 crayon curl DBI dbplyr DelayedArray deldir dplyr fansi farver fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr polyclip purrr R6 RANN RColorBrewer Rcpp rjson rlang RSQLite S4Arrays S4Vectors scales SingleCellExperiment SparseArray SpatialExperiment spatstat.data spatstat.geom spatstat.random spatstat.univar spatstat.utils stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

spaSim vignette

Yuzhou Feng, Anna Trigos

Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-11-29
Started: 2022-02-17

Citation

Development and contributors

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