Question: Cytoscape 3.3.0 visualize network with up/down regulated color
gravatar for bharata1803
4.4 years ago by
bharata1803470 wrote:


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.

cytoscape • 3.6k views
ADD COMMENTlink modified 4.4 years ago by Jean-Karim Heriche23k • written 4.4 years ago by bharata1803470
gravatar for Jean-Karim Heriche
4.4 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

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.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Jean-Karim Heriche23k

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:

ADD REPLYlink written 2.5 years ago by xanderpico290
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