Comments (3)
jpjarnoux
commented on June 19, 2024
Hi,
I don't see any reason why there is different information. I will look for the reason.
It's possible to share your both pangenome.h5 file ?
Thanks
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axbazin
commented on June 19, 2024
Hi,
Can it be additional info added by Gephi then saved into the gexf file by Gephi? It sounds like metrics computed after the original gexf file writing, I don't think that there is any code dedicated to finding triangles or weighted degree in ppanggolin.
Adelme
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ggautreau
commented on June 19, 2024
Hi,
Sorry for the delayed answer, did not see the issue before.
As said by @axbazin, Number of triangle, Degree and Weighted degree are metrics only added by Gephi. Maybe in some case you computed these statistics using Gephi and not in the others cases.
However, I think it would be easy to add them to PPanGGOLiN in a next version if there is a need for that.
Best regards.
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Related Issues (20)
- Error when re-partitionning a .h5 file obtained from the panmodule subcommand HOT 1
- Extract gene IDs located within RGPs HOT 4
- Only extract gene families within RGPs HOT 5
- Attribute error when draw spots HOT 2
- Deprecated NumPy HOT 5
- Identity/coverage threshold for species/genus? HOT 1
- Spot Plot Error HOT 2
- PPanGGOLiN hangs when partitioning does not work HOT 11
- doubt about Circular contig identifiers HOT 4
- Non-deterministic clustering (possibly due to defragmentation) HOT 11
- Attribute error drawing plots HOT 1
- Discrepancy between # of genes in RGPs? HOT 1
- Rarefaction curves_No Heaps calculation HOT 5
- RGP drawn in spot figure is incorrect HOT 3
- Locus tag missing from projection file HOT 2
- Gbk files HOT 4
- ppanggolin draw --spots all don't create plots for all spots HOT 6
- Projection file returns spots for genes not in RGPs HOT 3
- Ignore genes during clustering HOT 2
- Comparing core genomes HOT 7
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