CreateSpatialList

This function extracts the 'Spatial Files' slot from a Spatial Simulation Object
and removes probability columns while converting 'Positive' and 'Negative' in
cell assignment columns to 1 and 0, respectively.

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

CreateSpatialList function

<dl><dt>sim_object</dt>
<dd>A <code>SpatSimObj</code></dd>
<dt>single_df</dt>
<dd>boolean as to whether to collapse the output list of data frames to a single data frame or not. default is <code>FALSE</code></dd>
<dt>multihit_action</dt>
<dd>string of value 'random', 'drop', or 'keep' for cells that are positive for multiple cell assignments</dd></dl>

Arguments

Get Spatial Files from a SpatSimObj — CreateSpatialList

<dl>

<dt>sim_object</dt>
<dd>A <code>SpatSimObj</code></dd>


<dt>single_df</dt>
<dd>boolean as to whether to collapse the output list of data frames to a single data frame or not. default is <code>FALSE</code></dd>


<dt>multihit_action</dt>
<dd>string of value 'random', 'drop', or 'keep' for cells that are positive for multiple cell assignments</dd>

</dl>

CreateSpatialList: Get Spatial Files from a `SpatSimObj`

Description

Usage

Value

Arguments

Details