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farrellja / URD

URD - Reconstruction of Branching Developmental Trajectories
GNU General Public License v3.0
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treeForceDirectedLayout error #63

Open hogan-choi opened 3 years ago

hogan-choi commented 3 years ago

Hello,

I am using your tutorial with my data, but to have an issue. I am trying to use treeForceDirectedLayout to generate the 3D plot, but am having the following error. Perhaps it's my fault but I cannot find where I made the mistake:

[1] "2020-08-03 03:00:46 : Starting with parameters fr 100 NN 2 D 9193 cells" [1] "Removing 0 cells that are not assigned a pseudotime or a segment in the tree." [1] "2020-08-03 03:00:46: Preparing walk data." [1] "Removing 6 cells that were visited fewer than 1 times by random walks." [1] "2020-08-03 03:00:47: Calculating nearest neighbor graph." [1] "2020-08-03 03:00:47: Preparing edge list." [1] "2020-08-03 03:00:52: Removing 0.9% of edges that are between segments with distance > 2" [1] "2020-08-03 03:00:52: Trimming cells that are no longer well connected." [1] "2020-08-03 03:00:52: 98.94% of starting cells preserved." [1] "2020-08-03 03:00:52: Preparing igraph object." [1] "2020-08-03 03:00:52: Doing force-directed layout." [1] "2020-08-03 03:02:16: Calculating Z." [1] "2020-08-03 03:02:18: Calculating local density." Error in data.frame(seg = segTerminal(object), name = object@tree$segment.names[segTerminal(object)], : arguments imply differing number of rows: 7, 0

When I test the data frame, I get the following:

data.frame(seg = segTerminal(axial.tree), name = axial.tree@tree$segment.names[segTerminal(axial.tree)]) seg name 1 1 Neurons 2 2 Astrocyte 3 3 Oligo 4 4 Mural 5 5 Microglia 6 6 Ependymal 7 7 Endothilial

xiatianjihao commented 3 years ago

Hi hogan-choi, I have met the same problem, did you have sovled it ?

farrellja commented 3 years ago

@hogan-choi @xiatianjihao

Hi, I'm sorry I can't help you without a reproducible example. Please submit a saved R session of your environment prior to running the command (i.e. Session > Save Workspace As... in RStudio), the exact command you're running, and a copy of your sessionInfo(). You'll probably have to transfer this via Dropbox/Google Drive / some other such method to me.