Tuesday 19 December 2023

Visualisation using Cytoscape of a PopPUNK database

Earlier I wrote about how I made a visualisation of my PopPUNK database using Microreact: see the blogpost here.

Today I'm going to tell you how I made a visualisation of the same PopPUNK database using Cytoscape.

I followed the instructions in the PopPUNK documentation, but I had to figure out a few little things. 

Here's what I did:

I had already installed Cytoscape (which you can download from the Cytoscape website on my computer). I opened Cytoscape on my computer.

Then I dragged the network file from PopPUNK (called something like myexample_cytoscape.graphml) into Cytoscape window on my computer. Cytoscape gave me a message "Creating Cytoscape network". It then asked me whether I wanted to make a network view, and I pressed "Cancel".

I then clicked on the "Import table from file" icon at the top left of the Cytoscape window (see the icon with a picture of a spreadsheet), and then selected the csv file from PopPUNK (called something like myexample_cytoscape.csv). I set the value of "Key Column for Network" to be "id".

I then clicked on "G" in the left panel of the Cytoscape window, to select the network. 

I then clicked on "Create view" in the top right panel of the Cytoscape window to create an image of the network. Cytoscape gave me a message "Perfuse Force Directed Layout... Applying Force-Directed...". It took a few minutes to create an image of the network. The image then appeared!

I wanted then to change the appearance of the image of the network, e.g. colour and size of the nodes. I went to the Style panel of the Cytoscape control panel (on the left of the Cytoscape window), and clicked on "Style" on the left (it is written side-ways). 

Then I selected the "Node fill" to be "by Cluster" (to colour it by PopPUNK cluster), and "Mapping type" to be "Discrete". I then right-clicked on the "Discrete mapping" heading and selected "Mapping value generators" to be "Random". 

I selected the "Shape" (of nodes) to be "Ellipse" and selected the Node width to be 25.0 and the Node height to be 25.0 (so that I get a circle for each node).

I tried clicking on "Export" under the network image, and clicking "Export network as image" but this seemed to crash Cytoscape! Instead the next time I found I could just zoom in on the network and make a nice screenshot, something like this: