# Joint Dimension Reduction and Spatial Clustering

## Documentation for package ‘DR.SC’ version 3.5

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

## Help Pages

dlpfc151510 | A human dorsolateral prefrontal cortex data
DR.SC | Joint dimension reduction and spatial clustering
DR.SC.Seurat | Joint dimension reduction and spatial clustering
DR.SC_fit | Joint dimension reduction and spatial clustering
drscPlot | tNSE or UMAP plot visualization
FindSVGs | Find spatially variable genes
gendata_RNAExp | Generate simulated data
getAdj | Calculate the adjacency matrix given the spatial coordinates
getAdj.Seurat | Calculate the adjacency matrix given the spatial coordinates
getAdj_auto | Calculate adjacency matrix by automatically choosing radius
getAdj_manual | Calculate adjacency matrix by user-specified radius
getneighborhood_fast | getneighborhood_fast
mbicPlot | MBIC plot visualization
read10XVisium | Read the spatial transcriptomics data measured on 10X Visium platform
readscRNAseq | Read the scRNAseq data measured on scRNA sequencing platform
RunWPCA | Run Weighted Principal Component Analysis
selectModel | Select the number of clusters
selectModel.drscObject | Select the number of clusters
selectModel.Seurat | Select the number of clusters
spatialPlotClusters | Spatial coordinates plot visualization
sp_means_Rcpp | Calculate column-wise or row-wise mean
sp_sums_Rcpp | Calculate column-wise or row-wise sum
topSVGs | Return the top n SVGs