Sometimes you want to work with smaller chunks of your graph, so you can look at various elements in isolation (or in combination). ItвЂ™s much easier now to figure out whatвЂ™s going on in our graph, but itвЂ™s still a lot to take in. When we left off, weвЂ™d learned to build a simple Cytoscape graph, style that graph, import a node list, and use node attributes to control visual elements of our graph. Get a unimodal network from a bimodal network.Tableau 2: Basemaps, data layers, and geolocation.Messing around with the Topic Modeling Tool.

As you can see in VizMapper, there are a multitude of options for coloring and otherwise changing your network.Here, we can see that the shared OTUs are colored yellow, and the not_shared OTUs are colored pink. Now you can click on Node Color and color each individually. With this information, make a new column in your real_node_table.txt where you label each OTU based on it being shared or not_shared, and each sample based on being a Control or Fasting sample. You can now use the COUNTIF function in Excel to find if each OTU is present in either the Control group only, the Fasting group only, or in both. In column C put your entire list of OTUs taken from the otu_table.txt.

Make a new excel sheet that contains where column A represents the OTUs seen in the Control group, column B represents the samples in Fasting group.

Open up your real_edge_table.txt in Excel.

Copy out all the OTU Ids seen in your study.

Convert your biom table to a classic otu table using the biom convert command.

For example, how can we color the otus that are shared between the Control and Fasting groups a different color than the otus that belong to just one treatment group? To do this, we can:

If you want to do anything more вЂњcustomвЂќ, you need to play around with your node and edge tables.

Change the Control color to blue, and the Fast color to bright green.

LetвЂ™s change the edge colors connect our Treatment samples to their otus, and our Control samples to their otus.

Make the samples size 50.0, and the otus size 10.0.

all the Samples, since in this case our samples have the same LinkerPrimerSequence. This will group all the OTUs together vs. At the moment, we can click on LinkerPrimerSequence.

In more complicated datasets, it would be a very good idea to open up your real_node_table.txt in Excel and add in columns that will make it very easy to group items together, like Samples and OTUs.

Unfortunately, if your computer freezes on this step, thereвЂ™s really nothing to do but restart Cytoscape and try again.

This may take a moment to process depending on the size of your network.

In the upper tool bar window, Select: Layout -> Cytoscape Layouts -> Edge-Weighted Spring Embedded -> eweights Click on the Global tab, and change the background color to black.

Repeat this to make the Treatment samples bright green, and the otus whiteД¬lick inside the Defaults window to bring up a вЂњDefault Appearance for defaultвЂќ window.

This will bring up a Pick a Color window вЂ“ letвЂ™s make the Control samples a blue.

Click: Control, then click on the вЂњвЂ¦вЂќ next to it.

Remember, the nodes in our network consist of both Samples and OTUs. You should now see the Treatment groups of вЂњControlвЂќ, вЂњFastingвЂќ or вЂњotuвЂќ pop-up just below Node Color. whether they are in the Control or Fasting group. LetвЂ™s color our Samples by Treatment, i.e.

Cytoscape seletion