# Spatial Interaction Markers

## Documentation for package ‘SpaceMarkers’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

curated_genes | Curated Genes for example purposes
findAllHotspots | Find hotSpots for all spatial patterns
findGenesOfInterest | findGenesOfInterest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes.
findPatternHotspots | Identify hotspots of spatial pattern influence
getIMScores | getIMScores
getInteractingGenes | Calculate Interaction Regions and Associated Genes
getOverlapScores | getOverlapScores
getPairwiseInteractingGenes | getPairwiseInteractingGenes
getSpatialFeatures | Load spatial features
getSpatialParameters | Read optimal parameters for spatial kernel density from user input or .json file
getSpatialParamsMoransI | Calculate the optimal parameters from spatial kernel density for cell-cell interactions
load10XCoords | Load 10x Visium Spatial Coordinates
load10XExpr | Load 10X Visium Expression Data
optParams | Optimal paramters of 5 patterns from CoGAPS.
plotIMScores | plotIMScores
plotOverlapScores | plotOverlapScores