Hi All, 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 reasonable (black, for instance!) one? Thanks kindly & cheers, FB
Hi Fernando -
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
invisible?).
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 the logo).
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!
See http://issues.jalview.org/browse/JAL-1086
I'll be dealing with it shortly, with any luck.
Jim.
···
On Thu May 10 16:35:29 2012, Fernando Bazan wrote:
On Thu, May 10, 2012 at 9:50 AM, Jim Procter <foreveremain@gmail.com > <mailto:foreveremain@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
reasonable
(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 !Jim.