| Mondrian, the Genome Data Mapper Software: Configuration Options |
Configuring the Color Gradient
By default, Cytoscape will automatically create a color gradient, based on the minimum and maximum values in the profile data file. For example, the copy_number.gbm sample data file is encoded with the following values:
- -2: homozygous deletion (both alleles lost)
- -1: hemizygous deletion (only one allele lost)
- 0: copy number normal
- 1: single copy gain
- 2: multi-copy gain (>1 extra copy)
Based on this profile data, Cytoscape will automatically create a blue → white → red color gradient. For example:
- dark blue indicates homozygous deletion
- light blue indicates hemizygous deletion
- white indicates copy number normal
- light red or pink indicates single copy number gain
- dark red indicates multi-copy gain (>1 extra copy)
If you an unsure of the meaning of a color, you can move your mouse over an individual cell within the heat map. For example, rolling over the dark red cell for ERBB3 shows a copy number value of 2, or multi-copy gain (>1 extra copy).
To customize the color gradient, select a data type, e.g. Copy Number Data or Expression Data, and click the "Configure Color Gradient" button.
You can then pick from three color themes, or set minimum or maximum values. You can also set the minimum or maximum values for the center color.
Tip: Gradient settings can also be set in individual data files.
Configuring the Heat map
The heat map is also completely customizable. For example, the steps below describe how to focus the heat map on copy number variation within just three genes and three samples. This is a three-step process:
First, configure the data type:
- Click Configure Heat map
- In the left panel, select the "Data Type" tab.
- In the right panel, select the "Constant Property" tab.
- Within the "Data Type" tab, click "Copy Number Data".
- Click the right arrow button to transfer "Copy Number Data" to the Constant Property tab.
Second, configure the gene list:
- In the left panel, select the "Gene" tab.
- In the right panel, select the "Row Property" tab.
- Within the "Gene" tab, click Gene list, and select one more more genes. Tip: to unselect all genes, click the Uncheck genes button in the center of the screen.
- Click the right arrow button to transfer the selected genes to rows.
Third, configure the sample list:
- In the left panel, select the "Sample" tab.
- In the right panel, select the "Column Property" tab.
- Within the "Sample" tab, click Sample list, and select one more more samples under "Copy Number Data". Tip: to unselect all samples, click the Uncheck samples button in the center of the screen.
- Click the right arrow button to transfer the selected samples to columns.
- Click "OK" to complete the configuration.
A screenshot of the customized heat map is shown below:
