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cole-trapnell-lab / monocle-release

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traverseTree function in monocle2 origins from which R package? #491

Open junjunlab opened 1 year ago

junjunlab commented 1 year ago

Hi, I am reading plotting.R source code of monocle2 for plot_multiple_branches_heatmap function. But I can't find traverseTree function which R package it is from. Could you give some tips? Thanks!

Here is the related code:

root_cell <- root_state_cells[which(degree(g, v = root_state_cells) == 1)]
    tip_cell <- branches_cells[which(degree(g, v = branches_cells) == 1)]

    traverse_res <- traverseTree(g, root_cell, tip_cell)
    path_cells <- names(traverse_res$shortest_path[[1]])

    if(cds@dim_reduce_type != 'ICA') {
      pc_ind <- cds@auxOrderingData$DDRTree$pr_graph_cell_proj_closest_vertex
      path_cells <- row.names(pc_ind)[paste('Y_', pc_ind[, 1], sep = '') %in% path_cells]
    }