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Gene Transfer

Overview

Evolview supports visualization of gene synteny.The annotation has the following mandatory properties:

  • !groups Provide the genes represented in the plot.
  • !Colors Provide the colors in which genes are represented.
  • !genetransfer_style visualization style selected by the user

Here is an quick example of two styles

Supported modifiers

Apart from the common modifiers such as those that are related to legends, Group Labels supports an additional modifier:

!groupLabel. The value of this modifier defines default settings for all group labels and can be any combination of the following, separated by a ",":

modifier alternative value description
color=pink any color name or valid html hex colors such as #FF0000 default color for group lines and labels; default = black
dir=0:1 0:1 or 1:0 or 1:1 The 1 represents the direction where arrow is placed in the plot
radius= 120 any number value above 0 The radius adjusts the curvature of the arc used by the gene transfer arrows
linewidth=2 any integer >= 0 set width of the line; default = 1; see examples below
linestyle=dashed if set, a dotted group line will be plotted; default is regular line; valid only when style=1; see examples below
bkcolor=colorname any color name or valid html hex colors such as #FFFF00 color for line

Data

Each line of the Data section usually consists two parts, separated by a TAB. The first part defines to where the label will be placed, it can be either:

  • names of two leaf labels, a source label and destination label separated by ":". These labels can either be single leaf or range of the leaves separated by ",", or
  • a name of a leaf label.

The second part specifics the 'label' (required) and optional settings for this label such as font color, size.

See below:

Visualization styles

Tree

(chicken,((mouse,rat),(chimp,human)));

Style-1

Style 1

(copy & paste the following contents to Evolview to view the visualisation results):

!genetransfer_style	1
mouse:human	dir=1:1,color=darkgreen,linewidth=3,radius=120
mouse,rat:chimp	dir=1:0,color=yellow,linewidth=3
mouse,chimp:chicken	dir=0:1,color=red,linewidth=3

Tree

(chicken,((mouse,rat),(chimp,human)));

Style-2

Style 2

(copy & paste the following contents to Evolview to view the visualisation results):

!genetransfer_style	2
chicken:human	dir=1:0,color=darkgreen,linewidth=6
mouse:chimp,human	dir=0:1,radius=260,color=red,linewidth=2
mouse,rat:chimp,human	dir=1:1,color=black,linewidth=2