Cytoscape 3.3.0 visualize network with up/down regulated color

Question

[bharata1803]

Hello,

So, I want to visualize my network with cytoscape. I generate my network using R and it is a csv file. The columns are gene source, type of relationship, and gene target. I have successfully generate the network and it is really nice.

I want to add information about gene expression from another table which will mention if a gene is up/down regulated and want to use different color (red for up, green for down, and white for no change). I can generate this file in a csv with 2 columns, gene and type (up/down/no change). How can I use this in Cytoscape? Thank you.

Answer 1

[Jean-Karim Heriche]

You upload your gene up/down file as an attribute file into cytoscape with File > Import > Table > File. In the menu, select the column corresponding to your genes as "key column for network" and select "node table columns" for "import data as". This will create a new column in your node table associating each node (gene) with the corresponding category (i.e. up/down) from the file. To visualize, you need to go to the control panel, select the style tab then the node style tab then fill color. As column, select your category column (i.e. up/down) then select discrete mapping and assign a color to each category i.e. select a green color for down, select a red color for up.

EDIT: This is for Cytoscape 3.2.

[xanderpico]

Great description. I'll just add that in the last step, when you're assigning colors to each category, you can alternatively right-click anywhere on that property, choose Mapping Value Generators, and then select a preset range of colors to automatically perform the assignment. This is helpful when there are many discrete values. This is all covered in the manual here: http://manual.cytoscape.org/en/stable/Styles.html#tutorial-2-creating-a-new-style-with-a-discrete-mapping