My friends, any ideas about how to get the similar plot to show the alternative RNA splicing? I myself have googled, and only found on-line editing tool: http://wormweb.org/exonintron
It is cool but not enough. For example, the double splash indicating appropriate length skipping.
Perl (GD::Graph), Bioperl (Bio::Graphics) cannot solve them, I'm afraid. Thus give me a hint please. Thank you~~~
I assume you want the process to be as automated as possible.
From graphics I have seen, I imagine that it is possible (painful perhaps but possible) to do what you describe in Perl (GD::Graph) and/or Bioperl (Bio::Graphics).
However, if you wish to avoid that approach you can also script the creation of arbitrarily complex line drawings in R. For example, here is an illustration of alternative expression that was created in R: UMPS ALEXA-seq example (saved as an SVG - view in FireFox for best results).
Another option is to use GenomeGraphs as a starting point and either modify the code or export a simple graph and polish it in Illustrator, Inkscape, etc. This approach is described with visual examples here: Plotting exons of a transcript using GenomeGraphs
I haven't tried this, but Annotation Sketcher looks like it offers the features you are interested in. I think you can modify the depictions of splice sites using a style file. And as a bonus there is a web interface to get you up and running quickly.
Great thanks to all of you. I've collected other tools in another page. My goal is to use Command-line interface to generate the isoform graph as much as I can, so that we can deal with large numbers of data. But as @vitis said, they are mostly polished by Adobe Illustrator (you may try open-source Inkscape as alternative) when sent to publication.
My original idea is to parse sequence features using modules of bioperl, and plot the isoform graph using GD::graph or even Bio::Graphics. But if we wish to draw elegant map, perhaps other professional data visualisation tools (not for bio-research) are needed. Maybe d3.js, etc. But such a big work may not be worth of try as all I want is simply an isoform graph :-D
I have tried to do this very thing with Bio::Graphics and found it too difficult for me. You can draw these gene structures to scale with XFig and LaTex. Have a look at Figure 4 of this paper for an example.
Have you tried GenomeTools? In "How to generate a simple isoform diagram", Zak says he did not succeed using that, but for me it worked. I remember I made some such plots using GenomeTools command-line interface.
Thanks~~ Yes I'm in favor of Command-Line Interface, though sometimes hard to do it. Thanks for your answers.