Leiden - script fail

[HowieJM]

Hi, thanks for this tool ;) A quick Q. I already ran InferCNV, HMM = T, on current "best", which is Leiden.

io2 = infercnv::run(io1,
                    cutoff=0.1, 
                    out_dir="cutoff0_1_res0_000375_HMM", 
                    cluster_by_groups=F, 
                    HMM=T, 
                    analysis_mode='subclusters',
                    tumor_subcluster_partition_method='leiden',
                    leiden_resolution=0.000375,
                    denoise=T,
                    sd_amplifier=2,
                    #up_to_step = 15, 
                    resume_mode = TRUE,
                    num_threads=14
) 

I used this for some downstream analysis, but I now want to make a phylogenetic tree, ideally without re-running all prior analysis steps. Your tool looks good. I ran the test fine. But on my data, it fails.

Here is a snippet from test, and from my data:

Test:

cell_group_name cell
Retinoblastoma.Retinoblastoma_sRetinoblastoma.1.1.1.1   GATTCAGAGACGCAAC
Retinoblastoma.Retinoblastoma_sRetinoblastoma.1.1.1.1   GGCCGATCAAGTTCTG
Retinoblastoma.Retinoblastoma_sRetinoblastoma.1.1.1.1   AACTCTTAGACGCTTT
Retinoblastoma.Retinoblastoma_sRetinoblastoma.1.1.1.1   CACATTTGTACAGCAG

Mine:

cell_group_name cell
all_observations.all_observations_s1    AAAGTGAAGTGGAAGA
all_observations.all_observations_s1    AACAACCTCAGTCTTT
all_observations.all_observations_s1    AACCACAGTTTGGGTT
all_observations.all_observations_s1    AACGGGACAAGCGCAA

For my one, I edited out the reference cells, and also prefixes like REL TN ahead of cell names. Nonetheless, the result of mine is:

,100.0

Where the test is like:

1,0.0
1.1,0.0,B
1.1.1,0.0,C
1.1.1.1,15.776699029126213,D
1.1.1.2,16.74757281553398,E
1.1.2,0.0,F
1.1.2.1,15.29126213592233,G
1.1.2.2,27.9126213592233,H
1.2,0.0,I
1.2.1,0.0,J
1.2.1.1,9.466019417475728,K
1.2.1.2,6.553398058252427,L

I guess the difference relates to the .1.1.1.1 etc format, where I have .1-15. Do you know if there is some way I can get round this, or a way I could make my file in the format?

Would be great to know, as would be very useful if it was possible to run this tool with the Leiden approach ..

[atzatsos]

I experience the same problem. I used Leiden partition for infercnv and used the "cell_groupings" file as input but I failed to draw phylogenetic trees. Any help will be greatly appreciated.

[andynkili]

@atzatsos, @JamesHowie14 I am not part of the Dev Team but I had the same issue and the fix that I used is write_phylo=T when running infercnv. It will produce a newick file "infercnv.observations_dendrogram.txt". Then you can run python newick_input.py to load that file to choose tree length and ouput name. The latter will yield the corresponding cell.grouping file that you have to put inside uphyloplot2/Inputs path.

Best, Andy