Trying to run plot_pseudotime_heatmap as described in the Monocle2 tutorial results in the following error with Monocle3: Error in checkForRemoteErrors(val) : 3 nodes produced errors; first error: trying to get slot "family" from an object of a basic class ("logical") with no slots The...
Hi, I am trying to use plot_pseudotime_heatmap to map the heatmap of our source, but it doesnt work in monocle. And there are no error and result. Someone said may be I need a raw data to as the cds-object. It doesnt work, too. Then I wa...
#plot-拟时基本作图plot_cells(cds_data, label_cell_groups = F,color_cells_by = "pseudotime",label_branch_points = F,label_roots =F,label_leaves =F,graph_label_size = 0,cell_size=2,trajectory_graph_color='black',trajectory_graph_segment_size = 2) 提取拟时与celltype结果: pseudotime <-...
ps("heatmap.pdf", w = 5, h = 16)plot_cells(cds, genes = gene_module_df %>% dplyr::filter(module %in% c(200, 169, 138, 22,17,91)), group_cells_by = "partition", color_cells_by = "partition", show_trajectory_graph = FALSE)ps("module.pdf")saveRDS(cds,file="cds.rds") ...
(minimal_branch_len=9.5,euclidean_distance_ratio=1), define_root=T, know_root=T, root_state="YSMP") #plot plot_cells(cds_data, label_cell_groups = F, color_cells_by = "pseudotime", label_branch_points = F, label_roots =F, label_leaves =F, graph_label_size = 0, cell_size=2...
replayPlot(plot) dev.off() } n_jobs <- 8 # 使用的线程数 1.创建monocle对象 sobj:Seurat对象 cell_type:已经注释好了细胞类型 orig.ident:批次信息 sobj_embed:UMAP降维信息,是数据框,行名是细胞,有两列分别对应两个维度 hvg:3000个高变基因用于后续降维 ...
4.Order cells in pseudotime along a trajectory 手动选择root需要根据自己的生物学背景知识 ## Learn a graph cds %<>% learn_graph() plot_cells(cds,trajectory_graph_segment_size =1.5, group_label_size =6,group_cells_by="cluster", color_cells_by ="cell_type", label_groups_by_cluster =FALSE...
AACAAGAAGTTGAAGTxTransitionalM10.8270419WeaklyactivatedM1Ctrl-2:AACAGGGCATATCTCTxInfiltratingmacrophage1.4714588Monocyte-derived infiltrating macrophageCtrl-2:AACGAAACAAGACCTTxTransitionalM10.9654185WeaklyactivatedM1Ctrl-2:AAGAACAGTGAGTGACxTransitionalM11.0523062WeaklyactivatedM1num_genes_expressedPseudotimeStateCtrl-2...
replayPlot(plot) dev.off() } n_jobs <- 8 # 使用的线程数 1.创建monocle对象 sobj:Seurat对象 cell_type:已经注释好了细胞类型 orig.ident:批次信息 sobj_embed:UMAP降维信息,是数据框,行名是细胞,有两列分别对应两个维度 hvg:3000个高变基因用于后续降维 ...
#plot-拟时基本作图plot_cells(cds_data, label_cell_groups = F,color_cells_by = "pseudotime",label_branch_points = F,label_roots =F,label_leaves =F,graph_label_size = 0,cell_size=2,trajectory_graph_color='black',trajectory_graph_segment_size = 2) ...