Closed mhjonathan closed 2 years ago
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
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
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.
Hi,
I'm using the PPanGGOLiN for visualizing physical location of gene families. I tried to make light_gexf networks using Gephi with 3 different datasets, and I find out that one of light_gexf file contains node information of Number of triangle, Degree, Weighted degree.. which are not included in other light_gexf files even though all they got through same commands and parameters (I confirmed that they have same parameters with command: ppanggolin info -p pangenome.h5 --parameters.
The information (Number of triangle, Degree..) are exactly what I'm looking for, so how can I get all these data from other datasets too?
Below is the commands for 2 datasets without containing the information:
ppanggolin annotate --anno MAGs_gff_Input.txt --output MAGs_all --cpu 30 ppanggolin cluster -p MAGs_all/pangenome.h5 --clusters MAG_GeneFamily_all.txt --infer_singletons --cpu 30 ppanggolin graph -p MAGs_all/pangenome.h5 --cpu 30 ppanggolin partition -p MAGs_all/pangenome.h5 --cpu 30 ppanggolin rgp -p MAGs_all/pangenome.h5 ppanggolin write -p MAGs_all/pangenome.h5 --regions --output -f MAGs_all ppanggolin spot -p MAGs_all/pangenome.h5 ppanggolin draw -p MAGs_all/pangenome.h5 --cpu 30 --output MAGs_all --tile_plot --ucurve --spots all -f ppanggolin write -p MAGs_all/pangenome.h5 --cpu 30 --light_gexf --output MAGs_all -f ppanggolin write -p MAGs_all/pangenome.h5 --cpu 30 --gexf --output MAGs_all -f ppanggolin module -p MAGs_all/pangenome.h5 ppanggolin write -p MAGs_all/pangenome.h5 --modules --output MAGs_all -f ppanggolin write -p MAGs_all/pangenome.h5 --spot_modules --output MAGs_all -f ppanggolin write -p MAGs_all/pangenome.h5 --csv --output MAGs_all -f ppanggolin write -p MAGs_all/pangenome.h5 --partitions --output MAGs_all -f
And this is the commands for the dataset containing the information:
ppanggolin annotate --anno MAGs_gff_Input_Case.txt --output MAGs_Case --cpu 30 ppanggolin cluster -p MAGs_Case/pangenome.h5 --clusters MAG_GeneFamily_Ac.txt --infer_singletons --cpu 30 ppanggolin graph -p MAGs_Case/pangenome.h5 --cpu 30 ppanggolin partition -p MAGs_Case/pangenome.h5 --cpu 30 ppanggolin rgp -p MAGs_Case/pangenome.h5 ppanggolin write -p MAGs_Case/pangenome.h5 --regions --output -f MAGs_Case ppanggolin spot -p MAGs_Case/pangenome.h5 ppanggolin draw -p MAGs_Case/pangenome.h5 --cpu 30 --output MAGs_Case --tile_plot --ucurve --spots all -f ppanggolin write -p MAGs_Case/pangenome.h5 --cpu 30 --light_gexf --output MAGs_Case -f ppanggolin write -p MAGs_Case/pangenome.h5 --cpu 30 --gexf --output MAGs_Case -f ppanggolin module -p MAGs_Case/pangenome.h5 --cpu 30 ppanggolin write -p MAGs_Case/pangenome.h5 --modules --output MAGs_Case -f mkdir MAGs_Case/spot_plots ppanggolin write -p MAGs_Case/pangenome.h5 --spot_modules --output MAGs_Case/spot_plots -f --cpu 30 ppanggolin write -p MAGs_Case/pangenome.h5 --csv --output MAGs_Case -f --cpu 30 ppanggolin write -p MAGs_Case/pangenome.h5 --partitions --output MAGs_Case -f --cpu 30