Trouble Importing KEGG pathways in cytoscape

[Sayantan Laha]

Hi,

    I am trying to import pathways into cytoscape. I have downloaded the .xml files for the specific pathways. I have Keggscape installed on cytoscape. I am trying to import the pathway in cytoscape by going to File -> Import -> Import network from file and selecting the .xml file. However, the pathway is not being imported as displayed in the kegg patthway database. For instance, I am trying to import this pathway (Attached file: Image 1), through its xml file, and this is what I am ending up with in cytoscape (File attached: Image 2). I have tried this with several pathways, but in each case I am ending up with superimposed nodes in cytoscape as shown in the attached image. please help.

Thanks,

Sayantan

[Scooter Morris]

Hi Sayantan,

  Because there are multiple types of network XML files, you need to specifically select "KEGG XML Files (KGML) (*.kgml, *.xml)" under "Files of Type:" before you select the file and click open.   This tells keggscape that it's supposed to handle it.

-- scooter

[Alejandra Miranda Carrazco]

Hi. I have the same issue. I am working with cytoscape v3.10.1 with KEGGScape (v0.9.1) and I am trying to import E. coli TCA cylce pathway (https://www.genome.jp/kegg-bin/show_pathway?eco00020). When I try to import the file I choose KEGG XML Files but I get something like Sayantan´s image 2. Do I need to download something else or am I doing something wrong?

Thanks,

Ale

[Scooter Morris]

No, I'm seeing the same thing.  For some reason, KEGGScape isn't correctly applying (or creating) the proper style.  The information is all there in the node and edge tables, but the style isn't getting setup properly.  You can get things to work right by going through and setting up passthrough mappings for the X_LOCATION, Y_LOCATION, Label, Fill Color, Width, and Height.  I got a reasonable network that way, although doing some edge mappings to get the right arrows would improve it.