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#marker genes 和scRNA一样得操作Spatial_integrated = PrepSCTFindMarkers(Spatial_integrated)Markers <- FindAllMarkers(object = Spatial_integrated, only.pos = TRUE, min.pct = 0.1,thresh.use = 0.1, verbose = T, assay = 'SCT')
current.cluster.ids <- c(0, 1, 2, 3,4, 5, 6, 7,8, 9, 10, 11,12, 13, 14, 15,16, 17, 18, 19,20, 21, 22, 23,24, 25, 26)new.cluster.ids_clusterLevel <- c("White matter", "Th1", "Th2", "GPi","Striatum", "V", "Hy", "Amy","II", "III", "IV", "Mol","Cort.sub", "I", "DG", "Rsp1&2","I", "Bla", "Rtn", "VI","Ent", "Cort.sub", "Vent", "Ep","Chor.plx", "Th3", "CA3")new.cluster.ids_regionLevel <- c("White matter", "Thalamus", "Thalamus", "GPi","Striatum", "Cortex", "Hypoth", "Amyg","Cortex", "Cortex", "Cortex", "Hipp.","Cort.sub", "Cortex", "Hipp.", "Cortex","Cortex", "Bla", "Rtn", "Cortex","Cortex", "Cort.sub", "Vent", "Cortex","Chor.plx", "Thalamus", "Hipp.")
Idents(Spatial_integrated) <- 'clusterLevel'SpatialDimPlot(Spatial_integrated, images = 'Early2',stroke=0.1, label = T, label.size = 4,label.box=F, label.color = 'black',repel = T)&scale_fill_manual(values = cols) &theme_bw()&theme(axis.text = element_blank(),axis.ticks = element_blank(),axis.title = element_blank(),legend.position = "none")&ggtitle("#Replicate2 Early")
SpatialDimPlot(Spatial_integrated,ncol = 3,cells.highlight = CellsByIdentities(object = Spatial_integrated, idents = c('II')))
DefaultAssay(Spatial_integrated) <- 'SCT'pdf('./Figures/figure4.pdf', height = 8, width = 12)SpatialFeaturePlot(Spatial_integrated, 'Ttr', ncol = 3)&theme_bw()&theme(axis.text = element_blank(),axis.ticks = element_blank(),axis.title = element_blank())dev.off()
#注意，基因集是listCASgene <- list(c("Trem2","C4b","Lyz2","Gfap","Cd52","Ctss","C1qc","H2-D1","Gpr17","Hsph1","Ctsz","Hist3h2a"))#计算评分Spatial_integrated <- AddModuleScore(object = Spatial_integrated,features = CASgene,name = 'CAS')#plot==figure9SpatialFeaturePlot(Spatial_integrated,features = c("CAS1"),alpha = c(0.1,1),ncol = 3,min.cutoff = 0,max.cutoff = 1)&theme_bw()&theme(axis.text = element_blank(),axis.ticks = element_blank(),axis.title = element_blank())
