`plot_cell_trajectory`函数包含以下参数: -`data`:表示数据集的变量,包含细胞的状态信息。 -`x`:表示绘制细胞轨迹图的x坐标数据。 -`y`:表示绘制细胞轨迹图的y坐标数据。 -`color`:用于表示细胞状态的颜色数据。 -`size`:细胞状态的大小数据。 -`alpha`:细胞状态的透明度。 -`shape`:根据细胞类型定义的形...
1. 从trajectory图中提取数据 p2$layers[[1]]$data > p2<-plot_cell_trajectory(object_used_monocle2.cds,cell_size=1,color_by="seurat_clusters",show_tree=T)>p2 '#示例一 > head(p2$layers[[1]]$data) source target source_prin_graph_dim_1 source_prin_graph_dim_2 target_prin_graph_dim_...
plot_cells(cds, color_cells_by="seurat_clusters", label_cell_groups=FALSE) 解读 一般来说,对于多数据集,如果亚群的分组存在明显的分离,则说明存在批次效应,这个图看上去没有,毕竟只有一个数据集 #cluster your cells #这里的聚类已经不再是单单的聚类,按照作者的说法,是把细胞进行分区,后去的轨迹分析都会...
% dividing all trajectory date into each trajectory date numTrajectories = numel(startIndices); trajectoriesX = cell(1, numTrajectories); trajectoriesY = cell(1, numTrajectories); trajectoriesF = cell(1, numTrajectories); for i = 1:numTrajectories if i < numTrajectories trajectoriesX{i} = XL...
Visualise a single-cell trajectory as a graph or dendrogram, as a dimensionality reduction or heatmap of the expression data, or a comparison between two trajectories as a pairwise scatterplot or dimensionality reduction projection. Here’s a summary of the different plotting functions for visualisin...
plot_cells(cds,color='cell_type_designation_label',show_trajectory_graph=FALSE,label_cell_groups=FALSE)Error:`data` must be uniquely named but has duplicate columns rlang::last_trace()<error/rlang_error>`data` must be uniquely named but has duplicate columns Backtrace:x1.+-(fu...
Thesetcommand resets the line width of the axes, to make them easier to see. Several new arguments have been added to theplot()function. The‘k−‘changes the plot color from its default value (a blue line, at least on our computer) to a black line. The‘LineWidth’, 2makes the ...
plot_complex_cell_trajectory.Rd plot_genes_branched_heatmap.Rd plot_genes_branched_pseudotime.Rd plot_genes_in_pseudotime.Rd plot_genes_jitter.Rd plot_genes_positive_cells.Rd plot_genes_violin.Rd plot_multiple_branches_heatmap.Rd plot_multiple_branches_pseudotime.Rd ...
The bird's-eye plot assigns a different color to each actor, based on the default color order ofAxesobjects. For more details, see theColorOrderproperty forAxesobjects. To remove all meshes associated with mesh plottermPlotter, call theclearDatafunction and specifymPlotteras the input argument....
Data Types: double | char | string | cell AcceptedSamplesColor— Color of accepted samples three-element row vector | hexadecimal color code | color name Color of accepted samples, specified as a three-element row vector, hexadecimal color code, color name, or a short name. By default, the...