Joint Dimension Reduction and Spatial Clustering


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Documentation for package ‘DR.SC’ version 2.9

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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