plot_genes_branched_pseudotime branch names

[mengchengyao]

Hi,Thanks for your great tools of monocle,.

When I used it with plot_genes_branched_pseudotime, I got the resulte of figure as follows, but I could not understand it, I do not know what was meaning of branch Y_71 OR Y_79? How can i change this name? What's the connection between state and branch names?

Best

[ondp15]

Hello Cole-Trapnell Lab,

Hope your day is going well. I wanted to check-in if any of you have an answer to this question posted above by semir2. I have the same question and we are trying to figure out what it means. Can you please help us and point us in the right direction?

Thanks :)!

[yduanBioinfo]

I have edited the buildBranchCellDataSet function in BEAM.R. Then the branch labels will be replaced by the states of compared. ` if (is.null(branch_labels) == FALSE){ if (length(branch_labels) != 2) stop("Error: branch_labels must have exactly two entries") names(paths_to_root) <- branch_labels } #Edited get_path_name <- function(x){ counts <- table(pData(cds)[x,]$State) paste(names(counts[counts>0]),collapse='_') } names(paths_to_root) <- unlist(lapply(paths_to_root,get_path_name))

########### for (path_to_ancestor in paths_to_root){ if (length(path_to_ancestor) == 0){ stop("Error: common ancestors between selected State values on path to root State") }
all_cells_in_subset <- c(all_cells_in_subset, path_to_ancestor) } `