treeForceDirectedLayout error

[hogan-choi]

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]

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

[farrellja]

@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.