需要的包

mamba install -y -c conda-forge -c bioconda -c r \

r-ggsci \

r-dplyr \

r-future \

r-seurat \

r-clustree \

r-cowplot \

r-data.table \

r-ggplot2 \

r-patchwork \

r-stringr \

r-qs \

r-matrix

读取

library(Seurat)
library(ggplot2)
## 首先读取表达矩阵数据
ct = Read10X("~/Desktop/project/建模项目/新辅空转/GSE252176 RAW/GSM7996201_SXR_1/raw_feature_bc_matrix/")
## 然后读取image信息
img <- Read10X_Image(image.dir = file.path("./GSE252176 RAW/GSM7996201_SXR_1/", 
                                           "spatial"), filter.matrix = TRUE) 
## 接着创建seurat对象

sceP <- CreateSeuratObject(counts = ct, assay = "Spatial") 
img <- img[Cells(x = sceP)] 
DefaultAssay(sceP = img) <- "Spatial" 
sceP[['slice1']] <- img
## 空间分布
plot2 <- SpatialFeaturePlot(sceP, 
                            features = "nCount_Spatial",
                            pt.size.factor = 2) 
ggsave(filename = "1-QC/FeaturePlot_nCount.pdf", width = 12,height = 6, plot = plot2)