空间转录组共定位分析的一种方法

主要是利用了Seurat’里面AddModuleScore函数。

View(project_A33@meta.data)
?AddModuleScore

ILC1_feature <- list(c(
                       'IL7R',
                       'CCR6','KLRB1',
                       'IFNG','IFNGR1','IFNGR2'))

project_A33 <-
  AddModuleScore(project_A33,ILC1_feature,nbin = 24,ctrl = 100,name = "ILC1_SCORE",
  seed = 1
)
project_A33$ILC1_status <- ifelse(project_A33$ILC1_SCORE1 > median(project_A33$ILC1_SCORE1),'high','low')

#GPR34
p <- SpatialFeaturePlot(project_A33,features = 'GPR34')
m <- p$data
m$cellnames <- rownames(m)

project_A33@meta.data <- merge(project_A33@meta.data,m,by = 'cellnames')

project_A33$GPR34_level <- ifelse(project_A33$GPR34 > median(project_A33$GPR34),'high','low') 


project_A33$ILC1_GPR34_LEVEL <- ''

project_A33$ILC1_GPR34_LEVEL[which(project_A33$ILC1_status == 'high' & project_A33$GPR34_level == 'high')] <- 'high-high'
project_A33$ILC1_GPR34_LEVEL[which(project_A33$ILC1_status == 'high' & project_A33$GPR34_level == 'low')] <- 'high-low'
project_A33$ILC1_GPR34_LEVEL[which(project_A33$ILC1_status == 'low' & project_A33$GPR34_level == 'high')] <- 'low-high'
project_A33$ILC1_GPR34_LEVEL[which(project_A33$ILC1_status == 'low' & project_A33$GPR34_level == 'low')] <- 'low-low'


project_A33$ILC1_GPR34_LEVEL <- factor(project_A33$ILC1_GPR34_LEVEL)

Idents(project_A33) <- 'area'
SpatialDimPlot(project_A33,cols = list('Tumor' = '#e6194b',
                                      'Border' = '#3cb44b',
                                      'Stroma' = '#ffe119'),image.alpha = 0)

Idents(project_A33) <- 'ILC1_GPR34_LEVEL'

SpatialDimPlot(project_A33
               ,cols = list('high-high' = '#e6194b',
                            'high-low' = '#3cb44b',
                            'low-high' = '#ffe119',
                            'low-low' = '#4363d8'),pt.size.factor = 1.7
               ,image.alpha = 0 )       
  
#样本中都高的spot在tumor中的占比

length(which(project_A33$area == 'Tumor'& project_A33$ILC1_GPR34_LEVEL =='high-high')) / length(which(project_A33$area == 'Tumor'))  

#样本中都高的spot在非tumor中的占比

length(which(project_A33$area != 'Tumor'& project_A33$ILC1_GPR34_LEVEL =='high-high')) / length(which(project_A33$area != 'Tumor'))  

出图效果

最后通过HIGH-HIGH的spot所占cluster/区域的百分比，来统计比较不同区域之间某种特征细胞占比分布。