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cbg-ethz / BnpC

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
MIT License
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how can I generate tree file #21

Open jeffchen2000 opened 1 year ago

jeffchen2000 commented 1 year ago

according to the readme, BnpC can generate a output tree file (did I misunderstand?) but when I run this: run_BnpC.py snp.input.txt -tr test.gv

I got error like below, it seems that BnpC is trying to read "test.gv": Traceback (most recent call last): File "BnpC/run_BnpC.py", line 296, in main(args) File "BnpC/run_BnpC.py", line 291, in main generate_output(args, results, data, data_names) File "BnpC/run_BnpC.py", line 232, in generate_output io.save_tree_plots( File "BnpC/libs/dpmmIO.py", line 226, in save_tree_plots pl.color_tree_nodes( File "BnpC/libs/plotting.py", line 324, in color_tree_nodes with open(tree_file, 'r') as f_in: FileNotFoundError: [Errno 2] No such file or directory: 'test.gv'

NBMueller commented 1 year ago

BnpC does not infer the tree structure (see also (this issue)[https://github.com/cbg-ethz/BnpC/issues/18]). The option --tr takes the (simulated) tree used for data generation and colors the tree nodes according to the inferred clusters.

Putting it as an output argument might be misleading: I moved it to the input arguments.

jeffchen2000 commented 1 year ago

Hi NBMueller Thanks for your quick response! Yea, moving it to the input arguments will be better. and also, thanks for providing me the information about generating a tree file from third part (which is actually what I wanted). now, can I use a tree file generated from third part (say CellPhy as you mentioned) for the argument --tr ?

NBMueller commented 1 year ago

the -tr argument takes an existing mutation tree (nodes are mutations) in graphviz format and colors the nodes according to the identified clusters.

Cellphy infers a cell lineage tree (nodes are cells), due to the different tree representation it cannot be colored with BnpC. infScite infers the mutation tree, it should work with its output tree therefore.