Instructions:
install cystoscope on to your computer
intro video:
https://www.youtube.com/watch?time_continue=1&v=ZwaTTCcA-fo&feature=emb_title
Basic things you can do in cytosacpe
start a network
change nodes shape
change layout
make sub graphs
There are 2 basics things you need to run a basic cytoscape session
A network file (edge file)
- this will tell you how the genes connect
A table file (this is a node file that has a list of genes)
Instructions form first cytpscape email
Use ‘Import network from file’ to load the network into cytoscape (the network file is the edge file)
Use ‘Import table from file’ to import the node data to the network (including network proximity z-score, cluster id (partition_rank), and seed_node identity).
Use ‘Import table from file’ to import the Mayo RNAseq p-values and beta values (DE file may be downloaded from synapse as we did before. The file we want is called ‘MayoRNAseq_RNAseq_TCX_CONvsAD_DEG_Simple.txt’. Make sure the ‘GeneName’ is used as the key during import. Can also repeat this with corresponding hippocampus file to see if the same patterns are present.
Map various properties to nodes
Node shape to seed_node (I usually set seed nodes to triangles and non-seed nodes to circles)
Map RNAseq beta value to node color (I usually set the range from -1 to +1, and the color scales from blue to white to red)
Map the node sizes and font sizes. I usually make the seed_nodes larger than the non-seed nodes
Make subgraphs out of each partition_rank value. I have found that using the ‘yFiles radial layout’ gives a nice view for the individual clusters- the students can install the ‘yFiles’ app in cytoscape.
Make sure all labels are readable, by manual adjustment of node position, once happy with all other pieces (only want to have to do this once).
About step5 making subplots
use the filter function to select the nodes you want in the subplot
go to files --> new network --> from selected nodes, all edges
(or just use fast key command N for mac once you have selected the desired nodes)