AFD_lineage_cds <- cds[rowData(cds)$gene_short_name %in% AFD_genes, colData(cds)$cell.type %in% c("AFD")] 函数plot_genes_in_pseudotime()取一小组基因,并显示它们作为拟时间函数的动态,你可以看到dac -1在其他两个基因之前被激活。 plot_genes_in_pseudotime(AFD_lineage_cds, color_cells_by = ...
plot_genes_in_pseudotime(cds[top_genes, ], color_cells_by = "cell_type", min_expr = 0.5, ncol = 2)ps("Top_Genes_Jitterplot.pdf", w = 9, h = 6)p <- plot_cells(cds, genes = top_genes, show_trajectory_graph = FALSE, label_cell_groups = FALSE, label_leaves = FALSE)p$...
如果想看具体的某几个基因随pseudotime变化的趋势,可以用函数plot_genes_in_pseudotime(): AFD_genes <- c("gcy-8", "dac-1", "oig-8") AFD_lineage_cds <- cds[rowData(cds)$gene_short_name %in% AFD_genes, colData(cds)$cell.type %in% c("AFD")] AFD_lineage_cds <- order_cells(AFD_line...
plot_genes_in_pseudotime(cds[Track_genes_sig,],color_cells_by="seurat_clusters",min_expr=0.5, ncol= 2) FeaturePlot图 p <- plot_cells(cds,genes=Track_genes_sig, show_trajectory_graph=FALSE, label_cell_groups=FALSE, label_leaves=FALSE) p$facet$params$ncol <- 5 ggsave("Genes_Featureplot....
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 ...
Hello, I performed trajectory analysis on a dataset containing human monocytes and its progenitor cells. When I tried to plot genes that changed expression over pseudotime I get a plot that looks like this: I checked counts for this gene...
$gene_short_name %in% track_genes_sig, colData(cds)$celltype %in% c("NK cells", "Adipocytes", "Monocytes")] #lineage_cds <- order_cells(lineage_cds) plot_genes_in_pseudotime(lineage_cds, color_cells_by="celltype", min_expr=0.5) # 细胞映射 plot_cells(cds, genes= track_genes_sig,...
5.plot_cells展示 代码语言:javascript 代码运行次数:0 复制 Cloud Studio代码运行 # color_cells_by 设置展示分组情况plot_cells(cds,color_cells_by="celltype")# genes参数可视化基因的变化plot_cells(cds,genes=c("TP53","CDK4","CDK6")) 这张图可以用于确认设定的num_dim数是否代表足够的变异,可以看到...
Hello, I generated a UMAP trajectory in Monocle3 and am able to plot any genes of interest across pseudotime no problem with plot_cell_trajectory. However, we would like to be able to discover new genes that are specifically expressed at...
plot_cells(cds, color_cells_by ="partition",group_label_size=6) ps("UMAP_partition.pdf") 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, ...