TRJECTORY analysis -< getMonocleTrajectories()

[A-legac45]

Hello,

I have this issue when trying to use getMonocleTrajectories in parallele I alrready run monocle3 on my dataset and it works. How can I also precise to do it on genescore and not geneexpressionmatrix? is it by using umap-atac and not umap_rna?

cds <- getMonocleTrajectories( ArchRProj = proj_subset, 
 name = "M_monocle_pseudo", useGroups = c("C1", "C2","C3", "C4", "C5"), principalGroup = "C1", groupBy = "new_cluster_namesatac_janv", embedding = "UMAP_ATAC",graphParams = list(use_partition = F, close_loop = F, learn_graph_control = list(minimal_branch_len = 25, ncenter = 1000)),  clusterParams = list(k = 10))

ERROR
Running Monocole3 Trajectory Infrastructure!
Adding Embedding
Clustering Embedding
Learning Graphs
Getting Principal Node
Ordering Cells
Plotting Results - Monocole3/Plot-Results-M_monocle_pseudo.pdf
Error in g$grobs[[legend]] : no such index at level 2

From monocle 3 (no cluster supervised) and archr trajectory which I perform previously by isolating the cells identified by monocle 3 such as

idxPassMAIT1 <- which(proj_mat$cells %in%cds_pseudo_indicesM)
cellsPassM <- proj_mat$cellNames[idxPassMAIT1]
ARCHR_M_MONOCLE1_NEW <- proj_mat[cellsPassM, ]

and then implemented

ARCHR_M_MONOCLE1 <- addTrajectory(
    ArchRProj = ARCHR_M_MONOCLE1_NEW, 
    name = "M_monocle_1preFilterQuantile_avril", 
    groupBy = "MONOCLEtraj_mars", 
    trajectory = trajectory_monocle_order, 
    embedding = "UMAP_ATAC", 
     preFilterQuantile = 1,## Paramètre pour afficher toutes les cellules dans pseudotimes
  postFilterQuantile = 1,## Paramètre pour afficher toutes les cellules dans pseudotimes
      reducedDims = "LSI_ATAC",
    force = TRUE)

I observe small differences this is why I wanted to try your new version;

I have two trajectory with the same origin which I would like to implement in the same archr project is that possible?

Many thanks

Anne-laure

[immanuelazn]

Hi @A-legac45! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

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