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EasyFig 3 - version 3.2.0

Easyfig

Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recodong of Easyfig 2 initially developped by Mitchell J. Sullivan [https://mjsull.github.io/Easyfig/]

Authors: LECLERCQ Sébastien - BRANGER Maxime

Licence

Creative Commons Attribution-ShareAlike 4.0 International

CC BY SA

CC BY-SA 4.0

Installation

On Linux/MacOS

Conda

conda env create -f requirements.yml
./Easyfig

You can also add 'Easyfig' to your PATH.

On Windows

Conda

Blast is not include on conda environment for Windows.
You need to install it by your own : https://www.ncbi.nlm.nih.gov/books/NBK52637/
Please pay attention to the Configuration section of NCBI tutorial to correctly configure your installation.
blast executable must be in your env PATH.

conda env create -f requirements_windows.yml

To launch Easyfig 3, you need to open an anaconda powersheel terminal, then load easyfig environment (conda activate easyfig) and finally run easyfig (python Easyfig.py).
These steps can be done in an executable .bat file.

Tutorial

  1. Loading sequences
  2. Defining some features
  3. Setting some decorum
  4. Managing legends output
  5. Generate your first figure

Interface

General

General settings are set on the top of the window. And you can access to more windows using tabs header.
See Descriptions options for more information

General panel

Image size

You can manually set the figure output width (the height is automatically determined by the number of sequences to print).
Left/right/top/bottom margins can also manually be determined independently.

Output path

The output path can be set by clicking on the dedicated icon. If it is not set while asking to "create figure", a prompt window will ask you to.

Create figure

Button to generate the figure in SVG format.

Saving/Loading

By clicking on the "Application" menu, you will be able to save your current setup (every sequences adn fields), or only the configuration (features, blas, legends except sequences). You will be also able to load previous savend project or configuration.

Sequences window

This window provides all parameters for each imported sequence.
The "General" line defines some common parameters that are used while drawing if no specific parameter is set for a sequence. (this is what a '-' means in a field) Sequences in fasta of genbank formats can be imported using the '+' icon. You can enable/disable a sequence draw with the active field.
See Descriptions options for more information

Sequences panel

Features window

This window provides all parameters for features. You can set as many as you want. Like sequences, the General line defines common parameters if a no specific value for a feature's field. You can enable/disable a feature with the selected field. You also can display or hide a specific feature in the legend if needed.
The field "filter" can be used to select only specific features using regex syntax.
This allow you to display specific names, locus or any syntax contained in genbank file. The "in field" parameter allow to reduce the scope if needed.
See Descriptions options for more information

Features panel

Blasts window

See Descriptions options for more information

Blasts panel

Legends window

This window allows you to manage the displayed legend on the figure. By default, only the scale is printed. You can easily enable or disable each type of legend and choose where to print them out. See Descriptions options for more information

Legends panel

Decorum window

This window allows you to manage some additional displays on the figure, like GC%, GCskew and sequence-specific scale.
This works like sequences and features panels. You can define common parameters or enable/disable each decorum. See Descriptions options for more information

Decorum panel

Example of generated figure

This example shows the figure generated with the above options

Example output

Description of all options

You will find below the description for every options fields available.

General

Option Description Values
Image width Define the exact size of the image width. This is a fix value. Integer
Figure path Define the output file path of the figure. -
Margins Define the exact margins size of the figure. Integer
Background color Define the background color of the image. -
Enhance graph Add some shadow effects to features Checkbox

Sequences

Option Description Values
Sequence name Name of the sequence Automatically filled by gbk/fasta sequence name
infos Provide information about the sequence -
active Uncheck to not consider this sequence on drawing Checkbox
height Define th height of the sequence on the image Integer
line width Define the sequence line width Integer
space below Define the space below the current sequence Integer
line color Define the color of the sequence line -
position Determine the position of the sequence (inline) left/right/center/best blast/custom
min Position to consider to start on the sequence (default=1) Integer
max Position to consider to end on the sequence (default=max) Integer or 'max'
reverse Check to reverse the sequence Checkbox
print label Uncheck to hide sequence label Checkbox
label type Select the information to print as label locus/species/description/locus+size/locus+species/locus+description
label position Select the sequence label position left/right/top/bottom/top-left/top-right/bottom-left/bottom-right
offset to seq Offset value between sequence and label Integer
label color Select sequence label color -
label size Define sequence label size Integer
print feat. label Check to display features labels Checkbox
feat. label type Select information to print as features label gene/product/note/locus_tag/mobile_element_type
feat. label position Define features label position top/middle/bottom
feat color Define features label color -
feat label size Define features label size Integer
feat label rot Define features label rotation (default=0) Integer

Features

Option Description Values
selected Allow you to select/unselect a feature for the drawing Checkbox
show in legend Determine if this feature will be show in legend Checkbox
type Select the type of feature CDS/gene/mobile_element
strand Select the strand of the feature none/lead up/lag up
shape Define the shape of the feature on the draw arrow/rectangle/frame/signal/range/rangeL
hatching Define the hatching of the feature on the draw none/hbar/hbar2/circle/crossed/crossed2/rain/diagonal/Rdiagonal/waved/dotted/crosses
height ratio Define the ratio of the feature comparing to sequence height Float
fill color Color of the feature -
fill Fill or not Checkbox
line width Line width Integer
line color Line color -
filter Using a regex to select some specific features by name/product or anything Regex
in field Fields to apply the regex filter any/gene/product/note/mobile_element_type
print label Print feature label or not Checkbox
label type Which label type to print gene/product/note/locus_tag/mobile_element_type
label position Position of the label Opposite/top/middle/bottom
label color Color of the label -
label size Size of the label Integer
label rot Rotation of the label Integer

Blasts

Option Description Values
Run BlastN -
Load file -
minimum length Integer
minimum similarity Integer
minimum e-value Float
distance to sequence Integer
color (min/max) -
reversed color Checkbox
opacity Float
outline matches Checkbox
show labels Checkbox
min. match size Integer
label color -
label size Integer
decimals Integer
Matches selection None/adjacent/All vs All/All vs one/Custom

Legends

Option Description Values
General display Display/Hide this legend Checkbox
Horizontal position Select the horizontal position of the legend left/middle/right
Vertical position Select the vertical position of the legend top/middle/bottom
Scaling Define a scale ratio for this legend. (default=0.3) Float
Font Size Define the font size of the legend Integer
Font color Define the font color of the legend -
Cols number Determine the exact number of columns to use to display features legend (default=1) Integer

Decorum

Option Description Values
selected Allow you to select/unselect the decorum for the drawing Checkbox
show on sequences This button opens a popup which allows you to select/unselect sequences to print this decorum Switches on popup
type Select which type of decorum to draw GCskew/GC%/scale
step Step size in bases for calculations Integer
window Window size in bases for calculations Integer
position Position of the decorum in relation to the sequence On sequence/above/below
height ratio Define the ratio of the decorum comparing to sequence height Float
line width Line width Integer
line color Line color -
reverse Reverse min/max position Checkbox
print label Print or not the decorum label Checkbox
label color Color of the label -
label size Size of the label Integer
label position Position of the label in relation to decorum left/right

Logo

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