# # = F——消息,警告= F,结果= F ------------------------------------------ 库(scRNAseq)肺< - ZilionisLungData()免疫< -肺使用&肺肺used_in_NSCLC_immune美元< -肺(,免疫)肺肺[,1:5000]exp.mat < < - -矩阵::矩阵(计数(肺),稀疏= TRUE ) ## ----------------------------------------------------------------------------- 签名< -列表(Tcell = c(“CD3D”、“CD3E”,“CD3G”,“张”,“TRAC”),骨髓= c(“CD14”、“LYZ”,“CSF1R”、“FCER1G”、“SPI1”、“LCK——”),NK = c(“KLRD1”、“NCAM1”、“NKG7”、“CD3D——”、“CD3E——”),Plasma_cell = c(“IGKC”、“IGHG3”、“IGHG1”、“IGHA1”、“CD19 -") ) ## ---- 消息= F = F的警告 ----------------------------------------------------- 图书馆(UCell)图书馆(修)修。- CreateSeuratObject(counts = exp.mat, project = "Zilionis_immune")- AddModuleScore_UCell(seurat. ucell)对象特性=签名,名字= NULL)头(seurat.object [[]]) ## ---- 消息= F = F的警告 ----------------------------------------------------- 修拉的。- NormalizeData(seurat.object)对象<- FindVariableFeatures(seurat. properties)对象,选择。Method = "vst"， nfeatures = 500)- ScaleData(seurat.object) seurat.object对象<- RunPCA(seurat。对象，npcs = 20, features=VariableFeatures(seurat.object))对象<- RunUMAP(seurat。对象，还原= "pca"， dims = 1:20, seed.use=123) ## ----宽度= 9,fig.height = 7, dpi = 60 ---------------------------------------- 图书馆(ggplot2)图书馆(拼接)FeaturePlot(修。对象,减少= " umap "、特性=姓名(签名 )) ## ----------------------------------------------------------------------------- 修拉的。对象<- SmoothKNN(seurat。对象，signature.names = names(签名)，reduce ="pca") ## ----wide=TRUE, dpi=60---------------------------------------------------- FeaturePlot(seurat.object, reduction = "umap", features = c("NK","NK_kNN")) ## ----warning=FALSE, fig.width=9, fig.height=7, dpi=60------------------------- genes <- c("CD2","CSF1R") seurat.object <- SmoothKNN(seurat.object, signature.names=genes, assay="RNA", reduction="pca", k=20, suffix = "_smooth") DefaultAssay(seurat.object) <- "RNA" a <- FeaturePlot(seurat.object, reduction = "umap", features = genes) DefaultAssay(seurat.object) <- "RNA_smooth" b <- FeaturePlot(seurat.object, reduction = "umap", features = genes) a / b ## ----------------------------------------------------------------------------- sessionInfo()