Three Column Color Map

Table of Contents

• Three Column Color Maps
  • Command line coloring options with three colomn color maps
  • A simple example
    • Color labels and branches
    • Color labels only
    • Color branches only
  • Without Tags
    • Color labels and branches
    • Color labels only
    • Color branches only
  • With Tags
    • Color labels and branches
    • Color labels only
    • Color branches only
  • Some with tags, some without tags
    • Color labels and branches
    • Color labels only
    • Color branches only
  • Valid but redundant
  • Invalid color map

Overview

See here.

Three Column Color Maps

The three column color map is used when you want to color labels and branches separately.

The three column color map has the following columns: name, label color, and branch color.

The following examples will all use the following Newick file.

(s1,(s2,(s3,(s4,(s5,(s6,(s7,s8)))))));

You can download the file here.

Command line coloring options with three colomn color maps

As in the two column color maps, we can specify whether to color labels, branches, or both at the command line. These options have a higher precedence than the color map itself. This means that the command line coloring options will override anything that is in the color map file. For example, if s1 is specified to have its label colored blue, and its branch colored red, but only the --color-branches option is passid to Iroki, any color specifications for labels in the color map will be ignored. The examples that follow will help illustrate this behavior.

A simple example

#Name	Label Color	Branch Color
s1	red	green
s2	blue	red

In this example, the label of s1 will be red while the branch will be green. Similarly, the label for s2 will be blue and the branch will be red.

Color labels and branches

Command line options: --color-branches --color-taxa-names.

Color labels only

Command line options: --color-taxa-names.

Color branches only

Command line options: --color-branches.

The last example was a simple one, but the color map is actually pretty flexible in the different ways that you can specify colors. Let's take a look.

Without Tags

Iroki will infer whether you want the label or the branch to be colored based on the column.

#Name	Label Color	Branch Color
s1	blue	red
s2	red	blue
s3	blue
s4	red
s5		red
s6		blue

Color labels and branches

Command line options: --color-branches --color-taxa-names.

Color labels only

Command line options: --color-taxa-names.

Color branches only

Command line options: --color-branches.

With Tags

Sometimes it is better to be explicit about what you are doing. Therefore you can use tags you can use tags to clarify things.

Regardless of the column that a color specification is in, if it has a tag, Iroki will use the tag to infer whether to color the label or the branch.

The following are all valid tags:

• label:red
• label:#ff0000
• branch:red
• branch:#ff0000

Here is an example of using tags.

#Name	Label Color	Branch Color
s1	label:blue	branch:red
s2	label:red	branch:blue
s3	branch:blue	label:red
s4	branch:red	label:blue
s5	label:blue
s6	label:red
s7		branch:red
s8		branch:blue

Color labels and branches

Command line options: --color-branches --color-taxa-names.

Color labels only

Command line options: --color-taxa-names.

Color branches only

Command line options: --color-branches.

Some with tags, some without tags

You can mix specifying colors with tags and without tags, and Iroki will know what to do.

#Name	Label Color	Branch Color
s1	label:blue	red
s2	label:red	blue
s3	blue	branch:red
s4	red	branch:blue

Color labels and branches

Command line options: --color-branches --color-taxa-names.

Color labels only

Command line options: --color-taxa-names.

Color branches only

Command line options: --color-branches.

Valid but redundant

This color map is valid, but each row has redundant color specification.

#Name	Label Color	Branch Color
s1	blue	label:blue
s2	branch:blue	blue
s3	label:blue	label:blue
s4	branch:blue	branch:blue

Invalid color map

This color map has rows which are all invalid because of ambiuguous color specification.

#Name	Label Color	Branch Color
s1	blue	label:red
s2	label:blue	label:red
s3	branch:blue	red
s4	branch:blue	branch:red
s5		label:blue
s6	branch:blue

Here are the reasons why each row is invalid...

• s1 and s2 specify both blue and red for label color
• s3 and s4 specify both blue and red for branch color
• s5 specifies both blue and black for label color
• s6 specifies both blue and black for branch color

Iroki will raise an error if your color map has any of the above ambiguities.