GenerateSpatialPattern

Generate a spatial point pattern within the simulation object's window using a Poisson point process.

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/>.

Fridley Lab

scSpatialSIM

A Point Pattern Simulator for Spatial Cellular Data

Alex Soupir

Christopher Wilson

Jordan Creed

Julia Wrobel

Oscar Ospina

Brooke Fridley

GenerateSpatialPattern function

<dl><dt>sim_object</dt>
<dd>A 'SpatSimObj' containing a window.</dd>
<dt>lambda</dt>
<dd>The intensity of the point pattern Default is 25.</dd>
<dt>...</dt>
<dd>Additional arguments passed to 'rpoispp'.</dd>
<dt>overwrite</dt>
<dd>boolean indicating whether or not to replace point patterns if they exist in object</dd>
<dt>gridded</dt>
<dd>boolean value to whether or not simulate the point pattern in a grid. See details for more.</dd>
<dt>grid_shift</dt>
<dd>the amount to move alternative columns down when gridded; between -0.5 and 0.5</dd></dl>

Arguments

Generate Spatial Point Pattern — GenerateSpatialPattern

<dl>

<dt>sim_object</dt>
<dd>A 'SpatSimObj' containing a window.</dd>


<dt>lambda</dt>
<dd>The intensity of the point pattern Default is 25.</dd>


<dt>...</dt>
<dd>Additional arguments passed to 'rpoispp'.</dd>


<dt>overwrite</dt>
<dd>boolean indicating whether or not to replace point patterns if they exist in object</dd>


<dt>gridded</dt>
<dd>boolean value to whether or not simulate the point pattern in a grid. See details for more.</dd>


<dt>grid_shift</dt>
<dd>the amount to move alternative columns down when gridded; between -0.5 and 0.5</dd>

</dl>

GenerateSpatialPattern: Generate Spatial Point Pattern

Description

Usage

Value

Arguments

Details

Examples