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 “custom”, you need to play around with your node and edge tables.Change the Control color to blue, and the Fast color to bright green.Let’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, there’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 whiteĬlick inside the Defaults window to bring up a “Default Appearance for default” window.This will bring up a Pick a Color window – let’s make the Control samples a blue.Click: Control, then click on the “…” next to it.Remember, the nodes in our network consist of both Samples and OTUs. You should now see the Treatment groups of “Control”, “Fasting” or “otu” pop-up just below Node Color. whether they are in the Control or Fasting group. Let’s color our Samples by Treatment, i.e.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |