Data from
Cell classification Analysis of Image-based Spatial Data in Seurat
This code was create with Voyager package
@Manual{, title = {Voyager: From geospatial to spatial omics}, author = {Lambda Moses and Kayla Jackson and Lior Pachter}, year = {2022}, note = {R package version 1.0.3}, url = {https://github.com/pachterlab/voyager}, }
Moses L, Jackson K, Pachter L (2022). Voyager: From geospatial to spatial omics. R package version 1.0.3, https://github.com/pachterlab/voyager
analis_sfe
Percentage of blank features per cell
Plot that zoomed in patch to visually inspect cell-cell contiguity
nCounts and nGenes have sizable positive Moran’s I’s
Plot the top genes with positive spatial autocorrelation
Plot top gene loadings in each PC
Many of these genes seem to be related to the endothelium??
Plot the first 4 PCs in space
Makeshift function to plot a zoomed in patch spatial structure in PC2 and PC3 at a smaller scale
