Annotation Precedence
With Iroki, we can quickly color branches and labels independently of one another, remap label names, and use numerical data to create color gradients all on the same tree. To try and keep things clear and explicit, Iroki has strict rules of precedence when applying more than one annotation to the same tree.
- Command line options (
--color-branches,--color-taxa-names) - Color map
- Biom file
Then after all the coloring annotation has been done, the name map is used to map names.
This means that any coloring specifications in the color map will override the color gradient calculated from the biom file.
Command line options have the highest precedence of all. So if you only pass --color-branches then regardless of whether or not the color map or biom file would have added color to labels, Iroki will NOT color the labels.
Any of the tree annotation spec files (color map, name map, or biom file) can omit any of the sequences in the Newick file. This allows for very granular control over annotating the trees. Let's look at an example.
The files for this tutorial can be downloaded from the following links: biom file, color map, name map, newick tree, and the resulting nexus file.
We will pass both --color-branches and --color-taxa-names so that we may focus on the interaction of the three annotation spec files with each other.
The files look like this
This is the iroki command used to generate the Nexus file.
iroki -bte -f annotation_order.newick -o annotation_order.nexus -i annotation_order.biom -c annotation_order.color_map -n annotation_order.name_map
Here is the resulting tree.
