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TF-Chan-Lab / panGraphViewer

Show pangenome graphs in an easy way
MIT License
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Miss showing of insertion graph when using GFA file ? #6

Open Dkyuan opened 1 year ago

Dkyuan commented 1 year ago

Hi, sir:

I'm using this great tool to show the graph from a subset gfa file [ which generated by vg tool: .vg file to .gfa file]. The region is Chr01:1-6000.

I got few questions: 1. Mistake in insertion When I checked the figure, one path seemed to stop at the first insertion and generated a second end [as below]: 图片 the second end is supposed to be conected with the noed with blue arrow I don't know whether it was mistaken in the raw .vg/.gfa file, or in the ploting process in PanGraphViewer.

  1. Cannot change to cytoscape ploting It seems that I can't find the ways to change to cytoscape ploting from: settings --> graph modification 图片

  2. Can we get straight line backbon? I find it is difficult to arange the nodes in a more readable way in vis.js, and I noticed that in the closed issue #2 , a new version was mentioned, I'm wondering if it is the one I used (the latest version installed two days ago)

this is the subset gfa file I used for ploting: 1_6k.gfa.txt

Thanks for your time.

Dkyuan commented 1 year ago

I checked the subset file 1_6k.gfa, it has missed some nodes [94, 95] and edges/links [93-94, 94-95, 95-96] in the insertion position, so it gave e new end. After i added a link 93-96 in the gfa file, it worked and gave a full loop in the insertion position.

rickyma1 commented 1 week ago

Sorry for overlooking your post, and thanks for suggestions.

(2) Thanks for suggestion. It looks good. As we are working on an update, it may be included. (3) Thanks for suggestion. We are checking if it can be done by vis.js

Dkyuan commented 1 week ago

Sorry for overlooking your post, and thanks for suggestions.

(2) Thanks for suggestion. It looks good. As we are working on an update, it may be included. (3) Thanks for suggestion. We are checking if it can be done by vis.js

Thanks very much.