gpcrviz / flareplot Goto Github PK

When one uploads a json and visualizes a flareplot (on the flareplot website), it is unclear which pairs of nodes are connected by a given edge. Upon hovering, the edge and the connected node are not being highlighted. They are being highlighted in the example flareplots but not in the uploaded flareplots. It would be great if you could fix this.

On the input page, links to the python files are broken.

Hi,

The current font makes the labels of same size (e.g. 4 letters) appear with varying sizes. Using fixed-width/monospace fonts can fix this problem.

Courier is a pretty standard fixed-width web-font.

Just an idea of a nice feature to implement a .svg download of the current view

Hello,

After creating a flareplot, how can I download it for use in a presentation, or download a single image? I see the documentation on embedding it into a webpage, but I don't believe that is what I am looking for.

Best,
Christian

Neighbor nodes are highlighted even if edge is faded out.

From Mariona:

The keys of resi_to_group and resi_to_name are residue positions at the protein sequence, from residue 1 to the last residue (ex. 390). However, the mdtraj “residue index” gives the residue position at the PDB file, starting by 0. Therefore, if in the PDB the first residue sequence number is the 38, what mdtraj considers as residue index 0 will be residue 38 at resi_to_group and resi_to_name dicts. That's why we obtained shifted numbering: the H bonds were being assigned at residues shifted some positions with respect to the correct ones.

Flareplot charting area:

• Swap the positions of the labels and tracks
• Between the node-label and the corresponding track rectangle, synchronize the following action: on-click result (make track clickable), on-hover result
• Add play-button to the time slider

Website:

• Broken link on homepage of Flareplot: https://gpcrviz.github.io/FlarePlot/gpcr_demo.html
• Lowercase on the URL link of Flareplot: https://gpcrviz.github.io/FlarePlot/
• Optimize screen space on home page: refer to mockup (picture)
• Clicking a demo or example should bring you to a new clean page
• 'Generate input' links on home page have different destinations
• New pages for uploaded files/examples
• Choose typeface for the website

For manuscript:

• GPCR interactome: cluster by protein family
• Use B2AR deactivation simulation as an example for time series section

Great visualization tool but would like see self to self edges. Great tool, met some of the team at Stanford two months ago.

{
  "edges":[
    {"name1":"ARG135", "name2":"ASP134", "frames":[0,1,2,3,4,6,7,8,9]},
    {"name1":"ASP134", "name2":"TRP161", "frames":[4,5,6,7]},
    {"name1":"TYR223", "name2":"ARG135", "frames":[4,5,6,9]},
    {"name1":"TYR223", "name2":"TYR306", "frames":[0,1,2,5,6,7,8]},
    {"name1":"TYR306", "name2":"VAL54",  "frames":[1,4,5,6,7,8]},
    {"name1":"TYR306", "name2":"TYR306",  "frames":[1,4,5,6,7,8]} 
  ]
}

Also, back button on create page should go to create page