For the covariation color scheme, I want to generate random colors so I don't have to worry about storing an index of colors for an unknown number of helices. I found a nice
algorithm at stackoverflow.com. I set up everything for the covariation color scheme and tried out the random color selection for each nucleotide.
Examples are below. I like the first example that uses pastels, but I worry that the colors are not distinct enough from each other. The problem with the second example is that the dark colors make it impossible to read the nucleotide; I could figure out how to make the text white in those cases.
Hi Lauren,
ReplyDeleteWhat metric are you proposing to use for colouring covariation? What ever it is, won't you want to use a colour palette that indicates degree of covariation. Eg. a heat-map or the rainbow spectrum (ROYGBIV). This seems more obvious to me than using random colours. Or have I missed something?
See for example the 'cov' tab here:
http://rfam.sanger.ac.uk/family?entry=RF00086#tabview=tab3
Hi Paul,
ReplyDeleteYou bring up a good point, especially since I asked you about this earlier! Right now I'm just trying to achieve coloring of helices, something like one of RALEE's main coloring modes. See the screenshot on the RALEE page: http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
Perhaps I should call this color scheme a different name? Maybe the "helix" color scheme? I do intend to have something that shows degree of covariation, but I'm not set on how to implement it. One way is to have another scheme that has coloring like a heat map, such as what you described in Rfam. Another is to have a display below the alignment, similar to the conservation display, except for degree of covariation instead.
Do my descriptions make sense?