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（reference：Li, Y., Jiang, M., Aye, L. et al. UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment. Nat Commun 15, 1200 (2024). https://doi.org/10.1038/s41467-024-45340-w）
我们也尝试复现了整个过程（从亚群分析到最后结果呈现），至于方法是否有效，可能还需要探讨，但是至少是一个思路。同时也跟数据有关，我们的结果并不能凸显！
setwd('/home/data_analysis/基因与通路富集相关/')library(AUCell)library(Seurat)load("~/data_analysis/基因与通路富集相关/uterus.RData")DimPlot(uterus, label = T)Epi <- subset(uterus,cell_type=="Uepi")#亚群分析DefaultAssay(Epi)="RNA"Epi.list<-SplitObject(Epi, split.by = "orig.ident")for(i in names(Epi.list)){Epi.list[[i]] <- NormalizeData(Epi.list[[i]], normalization.method = "LogNormalize")}for(i in names(Epi.list)){Epi.list[[i]] <- FindVariableFeatures(Epi.list[[i]], selection.method = "vst", nfeatures = 4000)}#cca intergratedEpi.anchors<- FindIntegrationAnchors(object.list = Epi.list, dims = 1:30,normalization.method='LogNormalize',reduction='cca')Epi.integrated <- IntegrateData(anchorset = Epi.anchors, dims = 1:40)Epi.integrated <- ScaleData(Epi.integrated, vars.to.regress = c("S.Score", "G2M.Score","percent.mt", "nCount_RNA"), verbose = T)Epi.integrated <- RunPCA(Epi.integrated, npcs = 40, verbose = FALSE)Epi.integrated <- RunUMAP(Epi.integrated, reduction = "pca", dims = 1:15)Epi.integrated <- FindNeighbors(Epi.integrated, reduction = "pca", dims = 1:15)Epi.integrated <- FindClusters(Epi.integrated, resolution = 0.3)# DimPlot(Epi.integrated, label = T)# install.packages("SCpubr")# library(SCpubr)color_plot <- c("#d2981a", "#a53e1f", "#457277", "#8f657d", "#8dcee2")names(color_plot) <- unique(Idents(Epi.integrated))do_DimPlot(Epi.integrated,legend.position = "none", colors.use = color_plot,pt.size = 0.8, label = T)
# install.packages('ggpie')library(ggpie)ggnestedpie(data = Epi.integrated@meta.data,group_key = c("seurat_clusters", "orig.ident"),count_type = "full",inner_label = F,outer_label_type = "circle", # 设置外层环形outer_label_pos = "in",outer_label_info = "all",outer_label_threshold = 10,r0 = 1,r2 = 2,inner_fill_color = c("#FF5744","#208A42", "#FCB31A"),outer_fill_color = color_plot)
