I am starting with Cytoscape and tried to reproduce the tutorial "RNA-Seq data network analysis" with the example data set (E-GEOD-30573) in Cytoscape version 3.9.1 on Linux Debian. However, the step where the nodes are colored by fold change, does not work for me; the nodes remain grey after pressing the "Apply Preferred Layout" button.
Also, when importing the table with the differential expression data, I do not have the option "query term" for "Key column for network". Instead, I have only 2 choices, "shared name" and "shared interaction".
See attached screenshot "DE_genes_no_query_term.png"
At this point, in the node table in the right lower quadrant of the workspace, the columns of the tabular file are displayed, but they are empty, which is obviously the reason for the nodes to stay grey (there are no data).
See attached screenshot ["DE_genes_after_table_import_columns_empty_nodes_grey.png"] (https://i.sstatic.net/GCe62.png)
Interestingly, when I then import the same table a second time, I can see more options for "Key column for network", including "query term", which I select. Only now, the columns from the imported file are filled with data in the node table.
Another step I need to do for a color-scaled display of the fold change values (which is not mentioned in the tutorial) is to adjust the color range of the orange-red color scale (0-10 or 2-10 works fine for me for this data set).
This is my first contact with Cytoscape, however, I am a quite experienced computational biologist, so I was wondering whether it is something about my installation or operating system or whether the tutorial is maybe incomplete to some extent?
Many thanks for your comments.
Best regards, Sophia
The reason you aren't seeing any colors is that you weren't able to successfully import the fold change data initially. The symptoms you are describing can happen if for some reason the Edge Table is selected initially rather than the Node Table.
Before you import your expression data, make sure you have the Node Table selected and you should see those values. Once that's done, you should be able to set a mapping between your DE values and the node color.
