How do I edit the colors of my heat map annotation track?

Annotations on tracks can use heat map coloring, where annotations are colored according to the value of a qualifier on those tracks.  Operations in Geneious that automatically produce heat map annotation tracks include expression analysis, where annotations can be colored according to the magnitude of differential expression; and CRISPR site finding, where guide annotations can be colored according to their specificity or activity.  

In Geneious Prime 2020.2 and later, heat map color schemes can be customized.  To change the default coloring, click the drop down arrow next to the track and select Color by / Heatmap.  


At the top of the Color Annotations window is the qualifier that the annotations will be colored by.  The coloring currently set will be shown underneath. 


If non-numerical / automatic numerical is selected, qualifiers with non-numerical values will be assigned a distinct color for each distinct value.  For qualifiers with numerical values annotation colors will automatically be set from the track color to a whitish version of the track color on a sliding scale between the highest and lowest values.  

For example if the range of possible values is 1.0 to 5.0, an annotation with value 4.0 will be a blend of 25% whitish track color and 75% the track color.

If custom numerical is chosen, annotations will be colored on a sliding numerical scale between the specified values.  

For example the screenshot above shows the default values for coloring CRISPR guide annotations by the specificity score.  

To edit the coloring, select the color bar you wish to change and click Edit.  You can edit the value assigned to that color, or change the color itself by clicking the color bar.  


When you have set the colors the way you want them, click OK and you should see the change reflected on the annotation track.  


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