# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- 设置,eval = FALSE -------------------------------------------------------- # 图书馆(igraph) #库(schex) #库(TENxPBMCData) #库(嘘)#库(残渣)#库(ggrepel) # #——负载,eval = FALSE --------------------------------------------------------- # tenx_pbmc3k < - TENxPBMCData(数据集=“pbmc3k”)# # rownames (tenx_pbmc3k) <——uniquifyFeatureNames (rowData ENSEMBL_ID美元(tenx_pbmc3k),构成了rowData (tenx_pbmc3k) Symbol_TENx美元)# # # - filter-cells eval = FALSE ------------------------------------------------- # rowData (tenx_pbmc3k)水户< - grepl美元(“^ MT - rownames (tenx_pbmc3k)) # colData (tenx_pbmc3k) < - cbind (colData (tenx_pbmc3k), # perCellQCMetrics (tenx_pbmc3k,# =子集列表(Mt构成了rowData (tenx_pbmc3k)水户美元)=))构成了rowData (tenx_pbmc3k) < - # cbind (rowData (tenx_pbmc3k), # perFeatureQCMetrics (tenx_pbmc3k)) # # tenx_pbmc3k < - tenx_pbmc3k [, ! colData (tenx_pbmc3k)美元subsets_Mt_percent > 50) # # libsize_drop < - isOutlier (tenx_pbmc3k总美元,# nmads = 3,类型=“低”,日志= TRUE) # feature_drop < - isOutlier (tenx_pbmc3k发现美元,# nmads = 3,类型=“低”,日志= TRUE) # # tenx_pbmc3k < - tenx_pbmc3k [, ! (libsize_drop | feature_drop )] ## ---- filter-genes,eval = FALSE ------------------------------------------------- # rm_ind < - calculateAverage (tenx_pbmc3k) < 0 # tenx_pbmc3k < - tenx_pbmc3k [!rm_ind ,] ## ---- 规范、消息= FALSE警告= FALSE, eval = FALSE --------------------------- # tenx_pbmc3k < -嘘:logNormCounts (tenx_pbmc3k) # #,暗淡的红,消息= FALSE,警告= FALSE, eval = FALSE ------------------------ # tenx_pbmc3k < - runPCA (tenx_pbmc3k) # set.seed (10) # tenx_pbmc3k <——runUMAP (tenx_pbmc3k dimred =“主成分分析”,传播= 1,# min_dist = 0.4) # #——集群,eval = FALSE ------------------------------------------------------ # snn_gr < - buildSNNGraph (tenx_pbmc3k使用。dimred = " PCA ", k = 50) #集群< - cluster_louvain (snn_gr) # tenx_pbmc3k集群< -因子(集群成员美元 ) ## ---- eval = FALSE -------------------------------------------------------------- # plot_hexbin_density_shiny (tenx_pbmc3k 10 50, dimension_reduction = " UMAP ") ## ---- eval = FALSE -------------------------------------------------------------- # plot_hexbin_feature_shiny (tenx_pbmc3k类型=“计数”,功能=“POMGNT1”,# action =“prop_0 min_nbins = 10, max_nbins = 50,dimension_reduction = " UMAP " # mod = " RNA ") ## ---- eval = FALSE -------------------------------------------------------------- # plot_hexbin_meta_shiny (tenx_pbmc3k坳=“集群”,# action =“多数”,min_nbins = 10, max_nbins = 50, dimension_reduction =“UMAP”)