allocateCells |
Annotate all cells with contour level of cell type-specific density. |
cellsInRegion |
Check which cells are in which regions |
computeDensity |
Perform kernel density estimation on SpatialExperiment |
contour2sf |
Draw a contour region on some density level |
corDensity |
Test for density correlation between two cell types. |
findROI |
Find ROIs based on cell type-specific densities via graph-based method. |
getContour |
Get contour from density |
getContourRegions |
Calculate areas between every two density levels |
grid2sf |
Combine grids in each ROI to a sf region |
gridDensity |
Perform kernel density estimation on SpatialExperiment for cell types of interest |
mergeROI |
Manually merge ROIs |
plotCellCompo |
Plot cell type composition in each density level of cell of interest. |
plotContour |
Plot contour lines. |
plotContourRegion |
Visualising an sf object (for internal use only at the moment) |
plotCorHeatmap |
Plot model statistics using heatmap. |
plotDensCor |
Plot density correlation between two cell types |
plotDensity |
Plot grid-based density. |
plotROI |
Plot ROIs on spatial. |
plotSpatial |
Plot cells based on spatial coordinates. |
postSelRegion |
Merge sel_region from the selectRegion function to SpatialExperiment. |
selectRegion |
Select region of interest from plot |
spe2PB |
Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object |