# # = 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 ----------------------------------------------------- 南加州爱迪生公司库(UCell)库(SingleCellExperiment) < - SingleCellExperiment南加州爱迪生公司(列表(数量= exp.mat)) < - ScoreSignatures_UCell(=签名,特性,分析=“计数”,名字= NULL) altExp(南加州爱迪生公司,”UCell ') ## ---- 消息= F,警告= F ----------------------------------------------------- 库(嘘)库(拼凑)# PCA sce < - logNormCounts南加州爱迪生公司(sce) < - runPCA (sce、规模= TRUE, ncomponents = 10) # UMAP set.seed南加州爱迪生公司(1234)< - runUMAP (sce dimred = " PCA ") ## ---- 无花果。宽度= 7,fig.height = 5, dpi = 60 ---------------------------------------- 锁相环< -拉普兰人(姓名(签名),函数(x) {plotUMAP (sce colour_by = x, by_exprs_values =“UCell point_size = 0.2) +主题(方面。率= 1)})wrap_plots(锁相环 ) ## ----------------------------------------------------------------------------- 南加州爱迪生公司< SmoothKNN (sce signature.names =姓名(签名),减少= " PCA ") ## ---- 无花果。宽= TRUE, dpi = 60 ---------------------------------------------------- < - plotUMAP (sce colour_by =“骨髓”,by_exprs_values =“UCell point_size = 0.2) + ggtitle(“UCell”)+主题(方面。ratio = 1) b <- plotUMAP(sce, color_by ="Myeloid_kNN"， by_express_values ="UCell_kNN"， point_size=0.2) + ggtitle("Smoothed UCell") + theme(方面。比= 1)| b ## ----------------------------------------------------------------------------- sessionInfo ()