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Gene Synteny

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.
  • !genesynteny gene display properties and visualization style provided by the user
  • !totgenes Total genes used for the plot.(should be same as total number of groups)

Here is an quick example

Supported Key-Value pairs

Key (case insensitive) Value Description
width=20 default value is 20 the width of gene is decided by user input or uses default pre-set value
height=10 default value is 10 the height of gene is decided by user input or uses default pre-set value
style=1 default value is 1 Default style is set to be 1,for other visualization users can choose other styles.
fillbg=1 value can b 1 or 0 the gene blocks can have filled background color or transparent.
strokecolor=blue the stroke color for the genes. the default color is same as the color of the gene background.
stroketype=line default value is the line Default style is set to be line,for other visualization users can choose dashlines.
fontcolor=black any color name or valid html hex colors such as #FF0000 default color of group labels; default = black; if omitted, uses 'color'
fontsize=12 any integer set font size; optional; default = 10
fontitalic=1 0 set font italic; optional; default = 0
textalign=middle start or end set text align; optional; default = middle; see the following examples
bkcolor=colorname any color name or valid html hex colors such as #FFFF00 default color for group background; default = lightblue

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, it can be either:

  • names of two leaf labels, separated by a ',', or
  • a name of a leaf label.
  • The second part specifics the 'label' (required) and second part provides the gene information(gane_name:direction).
  • The directions can 0: unknown direction,1:left arrow,2:right arrow

See below:

Visualization styles

Tree

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

Style-1

Style-1

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

Example-1
Example 1

!groups	g1,g2,g3
!Colors	red,green,blue
!genesynteny	style=1,fontcolor=black,fontsize=8
!totgenes	3
!showGeneLabel	0
!showGeneDirection	1

A	g1:1,g2:0,g3:0
B	g1:1,g3:1
C	g2:0,g3:1
D	g3:2
Example-2
Example 2

with !showGeneLabel 1 prints the gene labels and absence of !showGeneDirection hides the direction information of the genes.

!groups	g1,g2,g3
!Colors	red,green,blue
!genesynteny	style=1,fontcolor=black,fontsize=15,width=40,height=20
!totgenes	3
!showGeneLabel	1

A	g1:1,g2:0,g3:0
B	g1:1,g2:2,g3:1
C	g1:2,g2:0,g3:1
D	g1:1,g2:0,g3:2

Style-2

Style-2

The style info is set using the style keyword in the gene synteny properties.

Example-1
Example 1

!groups	g1,g2,g3
!Colors	red,green,blue
!genesynteny	style=1,fontcolor=black,fontsize=8
!totgenes	3
!showGeneLabel	0
!showGeneDirection	1

A	g1:1,g2:0,g3:0
B	g1:1,g3:1
C	g2:0,g3:1
D	g3:2
Example-2
Example 2

!groups	g1,g2,g3
!Colors	red,green,blue
!genesynteny	style=2,fontcolor=black,fontsize=8,width=40,height=18
!totgenes	3
!showGeneLabel	0
!showGeneDirection	1

A	g1:1,g2:0,g3:0
B	g1:1,g2:2,g3:1
C	g1:2,g2:0,g3:1
D	g1:1,g2:0,g3:2