toy_ldata

A small synthetic dataset mimicking multiplexed tissue imaging data.
It contains one sample named "ToySample" with columns required by tlsR functions.

datasets

Fast, reproducible detection and quantitative analysis of tertiary lymphoid structures (TLS) in multiplexed tissue imaging. Implements Independent Component Analysis Trace (ICAT) index, local Ripley's K scanning, automated K Nearest Neighbor (KNN)-based TLS detection, and T-cell clusters identification as described in Amiryousefi et al. (2025) <doi:10.1101/2025.09.21.677465>.

Ali Amiryousefi

tlsR

Detection and Spatial Analysis of Tertiary Lymphoid Structures

Jeremiah Wala

Peter Sorger

toy_ldata function

A named list with one element:<dl>
<dt>ToySample</dt>
<dd>A data frame with columns:<ul>
<li>x: x-coordinate in microns</li>
<li>y: y-coordinate in microns</li>
<li>coarse_phen_vec: Cell phenotype ("B cells", "T cells", or "Other")</li>
<li>row_index: Integer row index (1 to nrow)</li>
<li>cflag: Integer flag column (0 for all cells)</li>
</ul>
</dd>
</dl>

Format

Toy multiplexed imaging data for examples — toy_ldata

A named list with one element:<dl>
<dt>ToySample</dt>
<dd>A data frame with columns:<ul>
<li>x: x-coordinate in microns</li>
<li>y: y-coordinate in microns</li>
<li>coarse_phen_vec: Cell phenotype ("B cells", "T cells", or "Other")</li>
<li>row_index: Integer row index (1 to nrow)</li>
<li>cflag: Integer flag column (0 for all cells)</li>
</ul>
</dd>


</dl>

toy_ldata: Toy multiplexed imaging data for examples

Description

Usage

Arguments

Format

Examples