A Point Pattern Simulator for Spatial Cellular Data
Compute Simulation Heatmaps
Create a spatial simulation object.
Get Spatial Files from a SpatSimObj
Get Simulation Parameters
Generate Cell Positivity
Generate Characteristic Distributions of Cells
Generate holes in a spatial simulation object
Generate Spatial Point Pattern
Generate Tissue
Pipe operator
plot function for SpatSimObj
Plot Simulation
Summarise Spatial
summary function for SpatSimObj
Update the simulation window in a SpatSimObj
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/>.