Joint Dimension Reduction and Spatial Clustering
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Documentation for package ‘DR.SC’ version 3.4
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 |