After some kind feedback from the Bergman Lab, we have released a new version of SVGmap, 1.5.0. In the Bergman Lab they are using SVGmap for displaying tissue-specific data of gene expression and insertion preferention of transposable elements in the drosophila and have written up a useful guide about how to install and use SVGmap. As you also can read in the same blog post, they have implemented a ‘stripped-down R implementation of the SVGmap approach, called FlyFig’.
Few months ago, Xavi and Michi wrote a post titled SVGmap: Configurable image browser for experimental data, which described a new tool developed in our lab. SVGmap is useful to create browsers for individualized high-quality images which change the color of some regions according to some values. For example, let’s say that you have expression data for various cell types in a particular tissue (or for various tissues in Drosophila, as in the image), you can draw an SVG image of the tissue showing each of the cell types and provide a tabulated file with the expression data, after few steps you can have a browser that allows you to search for particular genes and display the SVG image with the colors corresponding to the expression of each gene for each cell type. You can see some examples in the SVGmap web.
Have you ever heard of SVG? Scalable Vector Graphics (SVG) is an open standard to design images and graphics that can be scaled to any size without loosing quality. SVG is also the focus of a tool that we have developed in our group to cover specific needs of a collaborative project with an experimental group. The need was to visualize the spatial distribution of the expression of selected genes in different tissues and cell types. Read the rest of this entry »