VennDIS v1.2

Reference:
Ignatchenko, V., Ignatchenko, A., Sinha, A., Boutros, P. C. and Kislinger, T. (2015), VennDIS: A JavaFX-based Venn and Euler diagram software to generate publication quality figures. Proteomics, 15: 1239-1244. doi:10.1002/pmic.201400320

Introduction

VennDIS (Venn Diagram Interactive Software) is a JavaFX based application for producing highly customized, publication quality Venn and Euler diagrams. It is able to perform two to five way comparisons and has a large array of customization features, such as: font, style and position of the labels, background colours, ellipse sizes and outline colours. VennDIS accepts the following types of data: Lists, Table, or Values to calculate overlaps and differences for graphical display. Based on data input the tool automatically determines the most suitable Venn or Euler diagram(s). Created diagrams can be saved as XML format for future modification, exported as high-resolution bitmap images (PNG, JPG and BMP image formats) or as Scalable Vector Graphics (SVG).

Getting Started

The following main window is displayed when VennDIS is started:
interface

The toolbar of the VennDIS main window contains the following elements:

	- Create new Venn\Euler diagram.
	- Edit data input for current Venn/Euler diagram.
	- Open previously saved diagramm.
	- Save diagramm as XML file.
	- Export diagramm as a bitmap image.
	- Current help.
	- Swich to full screen mode.

Usage

Click on

to Create a new Venn\Euler diagram. The following data input window will appear:

data_input_lists

Three data input methods are currently available from the bottom right-hand corner toolbar. The desired input method can be chosen by clicking on the corresponding icon.
data_input_types_btn

By default the Lists input method is selected.

Lists-based data input

Lists-based input enables to submit (Copy/Pasted) lists of various identifiers for one or more datasets. Pasted identifiers are matched and values for differences and overlaps are calculated by VennDIS. Names for the individual datasets can be assigned at this stage (top header of the input column) or latter through the main interface.
data_input_lists

Table-based data input

Table-based input enables to submit tab delimited tables of values. Data can be either Copy/Pasted from the clipboard or imported as tab delimited text files by clicking the Import button on the top right-hand side of the toolbar. From the dropdown menu users can than select the appropriate columns for graphical display. Data imported as tables is considered binary data by VennDIS. Hence, any values present in the cells indicate the presence of this identifier in the current column/dataset. Alternatively, any empty cell or 0 values indicate the absence of this identifier.

data_input_table

Fasta-based data input

Fasta-based input enables user to search peptides against up to five fasta sequence databases. Algorithm will calculate number of peptides which are match to a single, or multiple fasta sequence databases.
Select one or more fasta files from right panel, paste the list of peptides to the input box on the left panel, and press Search button. After search is complete possible variations of available venn/euler diagrams will be displayed as icons on the bottom panel.

data_input_fasta

Notes:
If option "L = I" enabled, leucine (L) and isoleucine (I) in the sequence will be consider as the same amino acid.

Values-based data input

Values-based input enables users to manually type pre-calculated numerical values for the overlaps and the differences of the Venn or Euler diagrams. These values will be passed to the main interface for customization and image export.
data_input_values

Possible variations of available Venn or Euler diagrams are displayed as icons on the bottom left-hand side of the data input pages (in the case of all four input options):
Venn_Euler

Following selection of the desired diagram option by clicking on the icon the user then clicks on the OK button on the right-hand side of that page:

The input window is closed and the user is taken to the main window for customization and image export. If no desired image option is selected, the default option “Venn diagram” is automatically selected.

Main window

After the input dataset is submitted, the right-hand side of main window renders the Venn or Euler diagram using default customization parameters.
main_interface

The left-hand side of the main window contains the following tabs:

B&O (Background and Overlap) tab allows to modify, background colour and transparency; font, size and colour of the values displayed in the diagram.
interface

Ellipse tabs allow to modify size (%), colour, transparency AND z-order of circles/ellipses, as well as, modify font size, style and colour of the headers.
tab_elipse

Notes:
Manual circle/ellipse size re-adjustment is only possible for 2/3-way Venn and 2-way Euler diagrams.

After all desired customization is complete the Venn/Euler diagram can be saved as a XML formatted file.
Saved files can be open by clicking on the Open button open

nd can be further modified or exported as bitmap images.
To save a generated Venn or Euler diagram as an XML file users press the Save As button Save As

on the top left-hand corner of the toolbar and a dialogue window will open. In this window users can specify the file name and folder where the Venn/Euler diagram will be saved and press the Save button on the bottom right-hand corner of this window.
saveas_window

In order to export a Venn or Euler diagram as a bitmap image users press the Export button on the top left-hand corner of the toolbar Export

. A export image dialogue window will open.
export_window

In the Export image window users can select image resolution and press the Export button. A save dialogue window will emerge and users will select the preferred image format (PNG, JPG, BMP or SVG), the file name and the folder where the image will be saved. By pressing the Save button the image will be saved.
export