Create Heat Map from Comparison

The Create Heat Map from Comparison tool builds a heat map from a Pairwise Comparison such as those generated by Create Average Nucleotide Identity Comparison tool.

To run the Create Heat Map from Comparison tool:

        Toolbox | Whole Genome Alignment (Image wga_folder_closed_16_h_p) | Create Heat Map from Comparison (Image ani_heatmap_16_h_p)

Once the tool wizard has opened (figure 6.1), choose the Pairwise Comparison table you would like to use.

Image wgaheatmapcomparison
Figure 6.16: Select a Pairwise Comparison table.

In the next dialog (figure 6.2), you can set the following parameters:

Image wgaheatmapcomparison1
Figure 6.17: Select the table types and clusters construction methods you would like to use for building the heat maps.

The Pairwise Comparison table input is either a distance or similarity matrix. The tool automatically detects the type of each table by checking the values on the diagonal: if the diagonal contains only zeros, then the table represents a distance matrix, otherwise a similarity matrix. If the table is distance matrix, a similarity matrix s is calculated as follows:

s[i][j] = min + (1 - t[i][j]) * (max - min) if the table is a distance matrix,

where t[i][j] is the relative value (between 0 and 1) found in the table in row i and column j,

and min and max are the minimum and maximum magnitude of the table.

A heat map (figure 6.3) is then created from the similarity matrix s according to the specified clustering options and using a hierarchical clustering algorithm. Note that the tool outputs a heat map for each chosen table type and its name contains the table type used.

Image wgaheatmapcomparison2
Figure 6.18: A Comparison Heat Map.

Metadata from the Pairwise Comparison is transferred to the map. Additionally, sequence metadata containing taxonomy information is added if this information was present in the inputs. You can learn more about heat map views here: