单细胞空间转录组分析

#Installation
devtools::install_github("satijalab/seurat", ref = "spatial")

library(Seurat)
library(SeuratData)
library(ggplot2)
library(cowplot)
library(dplyr)

InstallData("stxBrain")
brain <- LoadData("stxBrain", type = "anterior1")

plot1 <- VlnPlot(brain, features = "nCount_Spatial", pt.size = 0.1) + NoLegend()
plot2 <- SpatialFeaturePlot(brain, features = "nCount_Spatial") + theme(legend.position = "right")
plot_grid(plot1, plot2)

brain <- SCTransform(brain, assay = "Spatial", verbose = FALSE)

SpatialFeaturePlot(brain, features = c("Hpca", "Ttr"))

p1 <- SpatialFeaturePlot(brain, features = "Ttr", pt.size.factor = 1)
p2 <- SpatialFeaturePlot(brain, features = "Ttr", alpha = c(0.1, 1))
plot_grid(p1, p2)

brain <- RunPCA(brain, assay = "SCT", verbose = FALSE)
brain <- FindNeighbors(brain, reduction = "pca", dims = 1:30)
brain <- FindClusters(brain, verbose = FALSE)
brain <- RunUMAP(brain, reduction = "pca", dims = 1:30)

p1 <- DimPlot(brain, reduction = "umap", label = TRUE)
p2 <- SpatialDimPlot(brain, label = TRUE, label.size = 3)
plot_grid(p1, p2)

# move your mouse
SpatialDimPlot(brain, do.hover = TRUE)

SpatialDimPlot(brain, cells.highlight = CellsByIdentities(object = brain, idents = c(1, 2, 5, 3, 4, 8)), facet.highlight = TRUE, ncol = 3)