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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.
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 ..
The text was updated successfully, but these errors were encountered:
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.
@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.
Hi, thanks for this tool ;) A quick Q. I already ran InferCNV, HMM = T, on current "best", which is Leiden.
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:
Mine:
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:
Where the test is like:
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 ..
The text was updated successfully, but these errors were encountered: