The Group Rows Table menu item is used to set advanced “groupings” for table rows. This can be used very effectively for coloring purposes, particularly when working with Inference Report data.
For instance, you could automatically color each variable (gene or probeset) in your chart by its p-value and fold change for one or more contrasts. It can be accessed by going to: Table | Rows | GroupRows.
Input Data Requirements
This command works on all Table objects, including Design Tables and Annotation Tables.
Step 1: Select the source table
The user will first be prompted to choose the table on which to group rows:
Step 2: Group
The Group Rows window is then presented. First, the user needs to add a grouping by selecting the "Add" button:
This will open the Edit Conditions window.
Step 3: Edit Conditions
In Edit Conditions, the user will specify numeric cutoffs, and columns to be considered for the cutoff, to define a group of variables.
The user can select one or more numeric columns, such as p-value or fold-change columns from an inference report; Multiple conditions can be set for each grouping.
Select a cutoff operator and value (e.g. <=.05), select whether Any or All of the selected columns should pass the threshold for the variable to be included in the group, and a label can also be created.
Once the parameters have been set for a group, click Okay. The user can define multiple groups by repeating this process.
After creating the groupings, the options include editing individual groups, removing groups, or clearing all groups. Clicking OK will finalize the grouping.
After grouping rows, the outcome won't be visible on the Table View itself. The user needs to go to a Volcano plot, or other View, of these data to see the result. Please refer to the Example Usage for detailed information. Groupings can be removed by going back to the Group Rows module and removing the desired groups.
We will use this inference table as an example. First, the inference report table is chosen:
And conditions are edited to add these two group labels, for Variables that have a p-value <=.05 in 1->DBP or 3->DBP, respectively:
After this, we can visualize the grouped rows in certain Views (for instance the Volcano Plot). Click Change Symbol Properties, set the Color By to Categorical, and choose the Probe Set ID (variable identifier) from the By drop-down box.
This will automatically color the plot using the specified groupings. Variables with p-value <=.05 in 1->DBP are colored green, while variables with p-value <=.05 in 3->DBP are colored blue; a third group of the variables that are in both groups is automatically made, colored cyan.