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DATASETS

BRANCH COLORS

Table of contents

Overview

Branch colors will be applied to tree branches.

Similar to pie charts, multiple datasets for branch colors can be uploaded to a tree, but only one can be shown at a time.

Here is an example:

Supported modifiers

Supported Key-Value pairs for branch colors:

Key (case insensitive) Value Description
!Groups or !LegendText comma separated text Legend texts; for example 'group_a,group_b,group_c'
!LegendStyle or !Style rect or circle or star shapes to be plotted before the legend texts; default = rect
!LegendColors or !Colors comma separated color codes or names colors to be applied to the shapes specified by LegendStyle; for example 'red,green,yellow' ; note the number of colors should match the number of legend fields
!Title or !Legend text title of the legend; default = name of the dataset
!ShowLegends 0 or 1 0 : hide legends; 1 : show legends
!opacity float number between 0 to 1 opacity of the dataset

Data

Data are usually tab-delimited three-column texts, with the third column optional. Let me use the tree below to illustrate the usage of the data:

(chicken,((mouse,rat),(chimp,human)));
  • first column: the location the first column dictates where the data to be plotted. It usually contains the name of a leaf node, or two leaf names separated by a ','.
  • one single leaf name dictates that the data will be plotted on / next to / under the leaf or the branch connecting directly to the leaf node
  • two leaf names, on the other hand, dictates that the data will be displayed on the branch representing the last common ancestor of the two leaf nodes

For example:

chicken
mouse,human
  • second column: color to be applied

For example:

chicken	green
mouse,human	blue
  • third column: optional commands to change the default behavior of current line

By default, the color will only apply to the specified branch; for example:

## branch color/ styles
human	red

By adding a third column, the default behavior can be changed. Here is a list of choices of this column:

Option (case insensitive) Description
ad apply color to all descendants
prefix apply color to all branches connecting leaf nodes whose name starts with the string specified by the first column
suffix apply color to all branches connecting leaf nodes whose name ends with the string specified by the first column
anywhere apply color to all branches connecting leaf nodes whose name contains the string specified by the first column
toroot apply color to all branches connecting the leaf node and parent nodes all the way to the root

See the examples below.

Examples

Example 1, 'ad':

## branch color
human,mouse	red	ad

Example 2, 'prefix':

ch	red	prefix

Example 3, 'suffix':

n	red	prefix

Example 4, 'toroot':

## branch color from specified leaf node to the root
human	red	toroot

add branch color to a collapsed tree

Evolview supports collapsing at internal nodes; collapsed nodes are treated as leaf nodes. It is therefore very straightforward to add branch color to a collapsed tree. See here for more information.