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Branch marker

Overview

Branch marker styles provide different ways to show the information using inner branches.The annotation properties can be provided in two formats:

  • !groups_class :Provides the annotation details for a specified group name or id.
  • Leaf/Branch based annotation details can provided for each leaf along with leaf Name.

Here is an quick example

Supported Key-Value pairs

Key (case insensitive) Value Description
text=group name to be displayed any textual/string content Provide a label name to be displayed for the annotation group.
id=some_unique_name any textual/string content without spaces Mandatory for using with !groups_class to represent the group annotation definitions.
shape=rect provide the shape The shapes can either be circle,rect,star,triangle,ellipse,check
width=20 provide the width of the shape(Mandatory) default width is set to be 20px. set the width and height as same for perfect positioning of the shape.
height=20 provide the height of the shape default height is set to be 20px. set the width and height as same for perfect positioning of the shape.
bkcolor=colorname any color name or valid html hex colors such as #FFFF00 default color for group background; valid only when style = 2~5; default = lightblue
fillbg=1 set the value either 1 or 0. defines whether the shape background should be transparent or filled; default = lightblue
color=pink any color name or valid html hex colors such as #FF0000 default color for group lines and labels; default = black
linewidth=2 any integer >= 0 set width of the group line; default = 1; if set to 0, the group line is hidden; see examples below
dashline=1 if set, a dotted group line will be plotted; default is regular line; see examples below

Data

Each line of the Data section usually consists two parts, separated by a TAB. The first part defines to where the group label will be placed, provide the inner branch name or provide all the leaf label names of a inner branch seperated by ",". To find the inner branch name, go to the tree and point the mouse on the inner branch.The tooltip will show the inner branch name.

The second part specifics the 'label' (required) and either provide group_class id or settings for this label such as font color, size.

Supported Shapes
triangle
circle
rect
star
check

Visualization styles

Tree

(A:0.1,(B:0.2,(C:0.3,D:0.4)100:0.05)100:0.1)90:0.43;
Example

Example 1

Placeholder

!groups	T1,T2
!Colors	red,green
!legendShapes	star,circle
##class def
!groups_class	id=T1,bkcolor=red,color=black,shape=star,width=20,height=15
!groups_class	id=T2,bkcolor=green,color=black,shape=circle,width=20,height=15

##data
INT2	T1
INT3	T2
Example

Example 2

Placeholder

!groups	T1,T2
!Colors	red,green
!legendShapes	star,star
##class def
!groups_class	id=T1,bkcolor=red,color=black,shape=star,width=20,height=15
!groups_class	id=T2,bkcolor=green,color=black,shape=star,width=15,height=15

##data
INT2	T1
INT3	T2
Example

Example 3

In this example we used different shapes and selected the inner branch using the branch leaf labels.

Placeholder

!groups	T1,T2
!Colors	red,green
!legendShapes	cross,check
##class def
!groups_class	id=T1,bkcolor=red,color=black,shape=cross,width=20,height=20
!groups_class	id=T2,bkcolor=green,color=black,shape=check,width=15,height=15

##data
INT2	T1
C,D	T2