[Jalview-discuss] Consensus Logo color change?
foreveremain at gmail.com
Thu May 10 20:30:24 BST 2012
Hi Fernando -
On Thu May 10 16:35:29 2012, Fernando Bazan wrote:
> Hi Jim, thanks for the quick response! I am indeed using the ClustalX
> coloring scheme for the alignment coloring, and this choice seems to
> set the Logo color to pink. If I choose another scheme, like Zappos,
> then you get a different Logo color (though some choices like Blosum62
> or Percentage ID appear to set the Logo color to white, making it
The philosophy here is that symbols in the logo get the same colour as
the symbols in the column. In the case of alignment based schemes like
percentage ID and ClustalX, the logo should reflect the colours of
residues as they are computed in each column, but a bug means that the
correct data isn't being passed to the routine that computes the colour
for the logo. Consequently, pink and white (default) colours are used,
which are fine if you have the Histogram displayed behind the logo, but
not much use otherwise! (you can enable the histogram independently of
> I think you're right that the Logo color is directly
> tied to the chosen color scheme, whereas it might be more useful to
> set it to a visible default (like black), or another user-defined
> scheme, independent of the alignment coloring.
yes - that would be the ideal, and I'm laying the foundations at the
moment for allowing more controls for the logo display style.
> So I'm guessing it is
> a bit of a bug.
and it also has a number - officially!
I'll be dealing with it shortly, with any luck.
> On Thu, May 10, 2012 at 9:50 AM, Jim Procter <foreveremain at gmail.com
> <mailto:foreveremain at gmail.com>> wrote:
> Hi there, Fernando.
> On Thu May 10 15:43:13 2012, Fernando Bazan wrote:
> I've just tried using the Logo option on the consensus
> annotation line, and it keeps on displaying the Logo with a
> pink or
> salmon color that is rather soft and faint, and quite difficult to
> view. Is there a way to change the Logo color to a more
> (black, for instance!) one?
> The colour for the logo is taken from the currently applied global
> colourscheme, or clustalX if no colourscheme is applied. It sounds
> like you've hit a subtle bug if the logo is only being coloured
> pink (which is the default 'invalid residue' colour from
> ClustalX). Try pressing escape and then changing the colourscheme
> for the view. If that doesn't help - I'll need to investigate further.
> If you could save your alignment as a project file and send it to
> me that would help me see what's going on !
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