Cytoscape visualization: Headings show up in the node table but not the data
Issue #69
new
Hello!
I am stuck at the Cytoscape visualization of the vcontact2 generated ‘c1.ntw’ file.
As per the instruction provided in the ‘Output files’ section of vContact2 https://bitbucket.org/MAVERICLab/vcontact2/src/master/ “Once ‘c1.ntw’ imported, a user can add an "annotation file" - that will be the genome_by_genome file. The annotation information for each genome will be added to each node/genome in the network. Then, the user can color the network figure by any attribute in the annotation file.“
In my case, after I import the ‘c1.ntw’ file and open it in Cytoscape following the instruction given in the protocol, https://www.protocols.io/view/applying-vcontact-to-viral-sequences-and-visualizi-x5xfq7n and then import the ‘genome_by_genome_overview.csv’ file, the headings show up in the node table but not the data.
Screenshots are attached below:
As per the recommendation provided in the issue ‘vConTACT2 Visualization in Cytoscape’ (https://bitbucket.org/MAVERICLab/vcontact2/issues/28/vcontact2-visualization-in-cytoscape) I have also incorporated a ‘Reference’ column in the ‘genome_by_genome_overview.csv’ file. ‘genome_by_genome_overview.csv attached.
I found a similar issue on the web: https://www.biostars.org/p/475400/ , but I couldn’t understand/ correlate the solution provided there.
Please guide me to solve the issue.
Regards
Adhip
Comments (1)
The “key” here is that you want to select Genome when “Importing Columns from Table.” You should be able to mouse-click on Genome, Order, Family, etc… (under the 3rd screenshot). That’s under the “Preview” and “Click a column to edit it”. There’s the key symbol, can you click/select Genome? It should let you change it to a key column. Cytoscape will then map the keys of your network using shared name with the Genome column, granting you the ability to select the network and color by attributes.
Let me know if that works.
-Ben