The Trajectory Summary is a great tool for viewing your data. Given a Cluster Labeling and a Gene Labeling, this tool will allow you to easily visualize and explore your data set.
Let's start by choosing 'Trajectory Summary' from the 'Analysis' menu. To start, select 'Cho Classification' for the 'Cluster Labeling'. So that we know which row (vector) represents which Gene, choose 'Gene Names' for 'Primary Labeling'. The 'Primary Labeling' is the labeling which is displayed when you click on an individual vector. Click 'Plot' when you are ready to view the Trajectory Summary.
Your 'Cho Classification' Trajectory Summary should look similar to the image below. You should have five clusters separating the gene expression data into five stages of the yeast cell cycle. The blue lines are the mean trajectory for a given cluster. The red lines are the standard deviation from the mean.
This is a helpful view to get an idea of what your clusters are doing, but if you want a more detailed view, click on the 'Plot All' button. In this case, lets look at the 'Late G1' cluster. Click on 'Plot All' for the 'Late G1' cluster now.
You should get a plot that looks like the following. The coloring of the trajectories is based on the expression level at time 0 by default. In a future version we may expose the ability to easily change the coloring schema within the GUI itself, but for now if you have the desire to change the coloring, you will have to use the 'Analysis Shell' which is discussed in section 3.6.
If you click on any point in the plot, a box in the top right will show up with the text 'Gene Name: (x-cord, y-cord)'. Click on the point shown in the diagram below and you should see 'SCW11: (10.00, 4.92)'. If you control click on the point shown below, a new dialog box appears showing the trajectory for 'SCW11' as shown in Figure 16 on the next page.
Note that at the bottom of the figure below, there are two Labelings, 'Gene Names' and 'Cho Classification'. If you click on the 'Gene Names' labeling you should see a pull down menu show up in the bottom right. If you then change this from 'default display' to 'Highlight This Group', this gene will be highlighted in your 'Late G1 - Plot All' display as shown in Figure 18 on the next page.
At this point you can 'Ctrl + Click' on other gene vectors and highlight them as well. This is all we will cover on the Trajectory Summary Plot for this tutorial. Feel free to explore more on your own or continue on to the next section of the tutorial.
Brandon King 2004-05-13