Closed muppi1993 closed 2 years ago
This should be done by this bit of code which masks the not-included nodes: https://github.com/johnlees/PopPUNK/blob/46aff5d5715b26a7582c733d6956cb4c78748a99/PopPUNK/plot.py#L488-L495
But maybe when we print the graphml it prints the masked nodes too? @nickjcroucher do you remember if this is the case?
All gets saved with the same function - masking can be a little tricky in graph-tool. Will take a look.
Also @muppi1993 highlighted that running with just --cytoscape
still generates a tree, which is not needed and quite slow - I think we should change this default, unless there any objections?
All gets saved with the same function - masking can be a little tricky in graph-tool. Will take a look.
I think we just need a GraphView
(adding in #204)
Also @muppi1993 highlighted that running with just
--cytoscape
still generates a tree, which is not needed and quite slow - I think we should change this default, unless there any objections?
Agree, will also add in 2.5.0
poppunk_visualise --ref-db poppunk_clusters --output cytoscape_5 --cytoscape --network-file /poppunk_clusters/poppunk_clusters_refs_graph.gt --include-files strains.csv --external-clustering meta.csv
I have the same issue when running this code -- several strains from the reference database are still included in the final cytoscape output even though it should just include the strains from the query/strain list
@johnlees @johnlees
Versions
poppunk 2.4.0 poppunk_sketch 1.7.4
Command used and output returned
Output: one .graphml and two .csv files
Describe the bug
I tried to only include a subset of the dataset in the output with --include-files, which worked fine for the --microreact output. However, the .graphml network contains all isolates from the database rather than just those listed in gps_cluster3_list.txt.