CNV Heat Map tab

The CNV Heat Map tab provides a visual representation of copy number variation (CNV) data in the form of a heatmap. You can select multiple analyses to compare the CNV data for multiple samples side by side. Ploidy values are used to quantify and compare call number variations. The ploidy value of 2 is expected for wild type samples where no genetic amplification or deletion was detected. A ploidy value of >2 indicates amplification. A ploidy value of <2 indicates deletion. In the heat map, a color scale is used to visualize ploidy, where the expected value of 2 is colored gray. For X and Y chromosome, the color that is applied to the plot considers the expected value given the gender. For example, for a male, the expected value for Y is 1, therefore, the cell for that variant appears as gray.

Use the menus in the Filter Options pane to limit the data that is displayed in the heat map. For a large data set, the data for the first 2,000 genes are retrieved.

  1. Click Selected Analyses to view the list of the analyses that are visualized.

  2. Heat map Filter Options.

  3. Heat map legend: ploidy. Hover over the legend the view the relationship between the ploidy value and the colors used in the heat map.

  4. Samples and analyses: hover over sample and analysis names to view the sample and analysis details.

  5. Genes: hover over a gene ID to view the details for that gene or click on the gene ID to view the details for all analyses in IRGV. Gene order is determined by the chromosomal position of the gene. The chromosome number is displayed to the left of the gene list.

  6. Variants: hover over a variant to view the details pane for that variant, or click in the cell to view the details for that variant in IRGV. If >1 CNVs are detected for the same gene, the number of CNVs is listed in the cell.

Use the following Chart Options to display the heat maps of choice and customize the heat map view.

Chart Option

Description

Scoring Function

The CNV heat map uses ploidy values to score copy number variants.

Gene Order

The CNV heat map orders the list of genes based on their position on the chromosome.

Sample Order

Select one of following options from the Sample Order dropdown list to arrange the order in which the genes are listed in the heat map.

  • Name: Samples are listed alphabetically by name from left to right.

  • Similarity: Samples are listed by how similar they are in the CNV calls made, presented from fewest to most CNV calls in common from left to right.

  • Similarity (left/right reversed): Samples are listed by how similar they are in the fusion calls made, presented from fewest to most CNV calls in common from right to left.

  • Analysis: Samples are listed alphabetically by analysis name from left to right.

Color Scale

Select a color scale to customize the colors that are displayed in the heat map.

Export Heatmap

You can export and save your heat map in PNG, SVG, and CSV file formats. The file is automatically downloaded once you make your selection from the Export Heatmap dropdown list.

Related Topics
Parent topic: Evaluate analysis results
Child Topics
Filter impact on the variants displayed in heat maps