Two Column Color Map
Table of Contents
Each of the examples for the two column color map will add color annotations to the following tree:
(s1,(s2,(s3,(s4,(s5,(s6,s7))))));
The newick file is available for download here.
In its simplest form, the color map has two columns name and color. The name refers to the label name of a leaf of the tree. The color can be specified as hex codes (e.g., #00FF00 for green) or as the name of a color. For a complete list of colors available to use in the color map file, see this page.
| #Name | Color |
|---|---|
| s1 | red |
| s2 | blue |
The color map file is available for download here.
In the above color map, the labels and branches of the sequences named "s1" and "s2" would be matched. However, whether label only, branches only, or both labels and branches are colored depends on the command line options passed in to the Iroki program.
Note: See here for more details on all available command line options.
To color both labels and branches, use these options
--color-branches
--color-taxa-names
and tree will look like this. (download it)
To color labels only, use these options
--color-taxa-names
and tree will look like this. (download it)
To color branches only, use these options
--color-branches
and tree will look like this. (download it)
Just like in the three column color map, you can use tags in the two column color map to restrict color to either branch or label.
Here is an example.
| #Name | Color |
|---|---|
| s1 | label:blue |
| s2 | branch:blue |
| s3 | blue |
This color map says: "Color the label of s1 blue, color the branch of s2 blue, and color both the branch and the label of s3 blue."
Of course, depending on the command line options passed to Iroki some of these directives may or may not happen.