Description

The aim of SVGMap is helping in the visualisation of experimental data which are associated with some graphical representation. Thus SVGMap browser allows to generate images with colored areas corresponding to the chosen data and color scale.

The data is represented as a table and is searchable. All data as well as the generated images/figures can be exported easily through the interface.

Additionally the tool allows to manage (add, edit or delete) experiments and configure the front-end user search appearance such as the number of images to be displayed, the scale types to use and more.

Quick start

You want to visualize your own data? These are roughly the steps you have to take:

  • Prepare SVG image. Use Inkscape (or a similar program) to create/modify your SVG image. Check if you can find an SVG image that fits more or less your needs in the wikimedia commons

  • Name regions of the image. If you use Inkscape, right click the SVG objects (regions) of the SVG image that your data refers to, select Object properties and give them the same ID as in your data file (cannot contain spaces)

  • Prepare the data file. The data file consists of various tab separated columns, (.tsv) where the first column is your region, the second the key (e.g. gene name) and all further columns are the data columns containing the value of the key in the region on the same row. Choose meaningful names for the first row of the file, which is considered the column header.

  • Execute SVGMap and access to the instantiated web server with your favorite browser at http://localhost:8095 where you can upload your example and browse it via:

    • click "Browse"
    • click "configure browser" (user: svgmap, password: svgmap)
    • click "Add new source"

    Instead of the first three step, use the examples in the folder svgmap/examples

Examples

We have included four examples to illustrate the diversity of data that can be represented. You can browse them in the browser section of our website or if you have downloaded the executable you may find them in the folder svgmap/exmaples folder

  • Drosophila: tissue specific differential expression
  • Copy number variation in cancer samples.
  • Cell cycle dependent expression in yeast
  • GO cell location: affected locations by misregulation in cancer

Download

Get the latest version of SVGMap:

Documentation and Contribution
SVGMap v. 1.4