Joint Dimension Reduction and Spatial Clustering


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Documentation for package ‘DR.SC’ version 2.4

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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 Adjoint matrix given the spatial coordinates
getAdj.Seurat Calculate the Adjoint matrix given the spatial coordinates
getAdj_auto Calculate Adjoint matrix by automatically choosing radius
getAdj_manual Calculate Adjonit matrix by user-specified radius
getAdj_reg Calculate Adjonit matrix for regular-distributed spots
HCC1 A liver dataset on Visium platform
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
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