laris package

LARIS - Ligand And Receptor Interaction analysis in Spatial transcriptomic data

A Python package for analyzing ligand-receptor interactions in spatial transcriptomics data.

LARIS provides tools for: - Calculating ligand-receptor interaction scores - Identifying spatially-specific ligand-receptor interactions - Inferring cell-cell communications

The package follows a modular structure: - laris.tl: Core analytical tools - laris.pp: Preprocessing functions - laris.pl: Plotting and visualization functions

Example usage:

>>> import laris as la
>>> import scanpy as sc
>>>
>>> # Calculate ligand-receptor interaction scores
>>> lr_adata = la.tl.prepareLRInteraction(adata, lr_df)
>>>
>>> # Identify spatially-specific LR interactions
>>> laris_results, celltype_results = la.tl.runLARIS(lr_adata, adata)
>>>
>>> # View top interactions
>>> print(laris_results.head(10))
>>> print(celltype_results.head(10))

Authors: Min Dai, Tivadar Török, Dawei Sun, et al. Version: 1.0.0

Subpackages

• laris.plotting package
  • plotCCCDotPlot()
  • plotCCCDotPlotFacet()
  • plotCCCHeatmap()
  • plotCCCNetwork()
  • plotCCCNetworkCumulative()
  • plotCCCSpatial()
  • plotLRDotPlot()
  • prepareDotPlotAdata()
  • plotCCCHeatmap()
  • plotCCCNetwork()
  • plotCCCNetworkCumulative()
  • plotCCCDotPlot()
  • plotCCCDotPlotFacet()
  • plotLRDotPlot()
  • plotCCCSpatial()
  • prepareDotPlotAdata()
• laris.tools package
  • prepareLRInteraction()
  • runLARIS()