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diogobor / XlinkCyNET

a Cytoscape app for visualizing cross-linking/mass spectrometry data
GNU General Public License v3.0
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Edges disappear when I annotate the protein domain to the nodes #2

Closed helloworld1631 closed 3 months ago

helloworld1631 commented 6 months ago

Hi, I used the exported .csv file from Scout v.1.4.14 and successfully loaded it to the Cytoscape. However, when I tried XlinkCyNET v1.5.2 to display protein domains following your video tutorial, I found cross-link edge cannot appropriately display. I tested the example file and it works well. So, I am wondering if there are any format issues with the exported file.

Thank you!

diogobor commented 6 months ago

Hello,

XlinkCyNET has been designed to take into account p-value scores (values between 0 and 1 -> the lower the better) for each CSM, residue pair and PPI. Scout had a bug that some times provides scores lower than 0. In these cases, the cross-link edges will not appear because of the filter. This bug were fixed and in the next Scout version you will be able to visualize all edges.

Meanwhile, you can change manually the score for the desired edges to a value between 0 and 1.

Best, Diofgo