Color Map
The color map file is where the magic of Iroki happens! In this tutorial we will explain how to make and use color maps with Iroki.
The color map file is a plain text file with two or three tab-separated columns.
Any line in the file that begins with a # will be treated as a comment and ignored.
Each of the following examples will add color annotations to the following tree:
(s1,(s2,(s3,(s4,(s5,(s6,s7))))));
Note: 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 |
|---|---|
| seq 1 | red |
| seq 2 | blue |
In the above color map, the label and branch of the sequence named "seq 1" would be colored red, while the label and branch of the sequence named "seq 2" would be colored blue.
Note: In the above example, whether label only, branches only, or both labels and branches are colored depend on the command line options passed in to the Iroki program. See here for more details.
Lets run the command to add color to the tree file.
iroki -bte -c basic1.color_map -f basic.tre -o basic1.nex
This will output a Nexus file called basic1.nex, which looks like this when rendered in FigTree.
