All functions

DR.SC_fit()

Joint dimension reduction and spatial clustering

DR.SC(<Seurat>)

Joint dimension reduction and spatial clustering

drscPlot()

tNSE or UMAP plot visualization

FindSVGs()

Find spatially variable genes

gendata_RNAExp()

Generate simulated data

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

dlpfc151510

A human dorsolateral prefrontal cortex data

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

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