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...
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 certain parts of the trajectory so we really need to be abl...
plot_genes_branched_heatmap -> genSmoothCurves -> responseMatrix 先看一下responseMatrix的源码,如下所示,可以发现报错点的if语句那里是有问题的。因为结合最开始的报错提示表明x@family@vfamily的长度可能不为1。 代码语言:txt AI代码解释 monocle:::responseMatrix function (models, newdata = NULL, response...
plot_cells(cds, genes=top10, show_trajectory_graph=FALSE, label_cell_groups=FALSE, label_leaves=FALSE) #这里官网还有一个筛选共表达模块,但是我觉得用处有限,这里就不展示了,感兴趣的同学可以访问下面官方教程 #https://cole-trapnell-lab.github.io/monocle3 #把我们细胞轨迹分析的结果返回Seurat对象中 ps...
I got an error from plot_trajectories, see below. I appended the program below the error message. ValueError Traceback (most recent call last) Cell In[1], line 239 237 print(solution.shape) 238 prob.plot_constraint_violations(solution) ...
I have tried with devtools::install_github("dynverse/dynplot@devel") Thanks for your time dat <- readRDS("mySeuratProject") dataset <- wrap_expression( counts = t(dat@assays$RNA@counts), expression = t(dat@assays$RNA@data) ) %>% add_grouping(dat$finClu) guidelines <- guidelines_shin...
+Some of this analysis and the concepts used here are similar to another +network analysis package called [SCENIC](https://github.com/aertslab/SCENIC), +but this TF regulatory network analysis included in hdWGCNA is a distinct +approach with key differences. Here, we demonstrate this analysis...
when I run: plot_genes_branched_pseudotime(cds[my_pseudotime_gene,], branch_point = 1, color_by = "celltype") I get: Warning in class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE : 'length(x) = 2 > 1' in coercion to 'logica...
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...
Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org - ucscGenomeBrowser/cellBrowser