Spatial Interaction Markers
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Documentation for package ‘SpaceMarkers’ version 1.3.5
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 |