error in scaffold map

[Terskikh]

Dear Federico,

I have the problem with generating of scaffold map. To show you an error I have attached this part of code here below. I would like to ask you if you have ever experienced the same proble. I would like to quickly explain how I prepare files for analysis. I take results of flowsom clustering and write txt and Rds files (the same format of file which can be generated by grapolo). I don't have any problems to make unsupervised graph. However when I add landmarks files I can't finish the analysis. Those files were written as flowSet and exported from R.

Thank you in advance!

vite::run_scaffold_analysis(input.files, ref.file = "clustered_single_samples/allevents.fcs.clustered.txt", landmarks.data, col.names)
Processing clustered_single_samples/allevents.fcs.clustered.txt
Running with Edge weight: 7.000000
Hard removing some connections to landmarks using threshold: 1.000000
First iteration
Stopping tolerance: 0.001000

Total number of iterations: 2844
Second iteration with prevent overalp
Stopping tolerance: 0.001000

Total number of iterations: 3141
Adding inter-cluster connections with markers:
ICAM PD_L2 CD163 ..........

Weight factor:0.700000
First iteration
Stopping tolerance: 0.001000

Total number of iterations: 13410
Second iteration with prevent overalp
Stopping tolerance: 0.001000

Total number of iterations: 3294

### Error in V(g.temp)$highest_scoring_edge[i] <- max.edge :
replacement has length zero

[pfgherardini]

You should write the landmarks data as FCS files and load them using the load_landmarks or load_landmarks_from_dir functions. If that's what you are doing already, then please share the dataset you have been working with (using Dropbox or similar) so that i can take a look