# #——global_options,包括= FALSE -------------------------------------------- knitr: opts_chunk美元集(警告= FALSE,消息= FALSE,包括= TRUE, fig.height = 8, fig.width = 8, fig.align =“中心”,回声= TRUE ) ## ---- 安装,eval = FALSE ---------------------------------------------------- # # BiocManager:安装(“猎犬 ') # # ## ---- 加载库 ---------------------------------------------------------- 库(猎犬)库(DropletUtils)图书馆(嘘)图书馆(残渣)# #——数量 ------------------------------------------------------------------- pathToTenXOuts < file.path(系统。文件(包=“猎犬”),南加州爱迪生公司“extdata /出局”)< - createVisiumSCE (tenXDir = pathToTenXOuts分辨率= "低 ") ## ---- 条形码 ----------------------------------------------------------------- colData (sce) [c(“条形码”、“pixel_x”,“pixel_y ")] ## ---- image_dimensions --------------------------------------------------------- 元数据(sce) grob ImgDims # #——美元 --------------------------------------------------------------------- Grob元数据(sce) $ # #——qcplotting,结果=“隐藏 "------------------------------------------- 过滤器检测到南加州爱迪生公司< - $ > 0 spanielPlot(对象= sce、plotType =“NoGenes showFilter =过滤器,techType =“Visium ptSizeMax = 3 ) ## ----------------------------------------------------------------------------- sce南加州爱迪生公司(< -、过滤 ] ## ---- 基因的阴谋,结果= "隐藏 "-------------------------------------------- 南加州爱迪生公司< - logNormCounts (sce)基因< -“ENSMUSG00000024843 p2 < spanielPlot(对象= sce plotType =“基因”,基因= " ENSMUSG00000024843 " techType =“Visium ptSizeMax = 3) p2 ## ----------------------------------------------------------------------------- 南加州爱迪生公司库(残渣)< - logNormCounts南加州爱迪生公司(sce) < - runPCA南加州爱迪生公司(sce) < - runUMAP (sce) g < - buildSNNGraph (sce k = 70) clust < - igraph:: cluster_walktrap (g)会员sce clust美元(clust < -因素 ) ## ----------------------------------------------------------------------------- p3 < - plotReducedDim(预计,“UMAP”,p3 colour_by = " clust ") ## ----------------------------------------------------------------------------- p4 < - spanielPlot(对象=,plotType =“集群”,clusterRes =“clust showFilter = NULL, techType =“Visium ptSizeMax = 1, customTitle =“节”)p4