Matlab: seqlogo with uniform plot column heights - matlab

Question

In Matlab, I want to make a seqlogo plot of an amino acid sequence profile. But instead of scaling the heights of the plot columns by entropy, I want all the columns to be the same height.
I'm in the process of modifying the code from the answers to this question, but I wonder if there is a parameter to seqlogo or some other function that I have missed that will make the column heights uniform.
Alternatively, is there a statistical transformation I can apply to the sequence profile to hack the desired output? (column heights uniform, height of each letter linearly proportion to
its probability in the seqprofile)

Answer 1

Probably the easiest way around this problem is to directly modify the code for the Bioinformatics Toolbox function SEQLOGO (if possible). In R2010b, you can do:
edit seqlogo
And the code for the function will be shown in the editor. Next, find the following lines (lines 267-284) and either comment them out or remove them entirely:
S_before = log2(nSymbols);
freqM(freqM == 0) = 1; % log2(1) = 0
% The uncertainty after the input at each position
S_after = -sum(log2(freqM).*freqM, 1);
if corrError
% The number of sequences correction factor
e_corr = (nSymbols -1)/(2* log(2) * numSeq);
R = S_before - (S_after + e_corr);
else
R = S_before - S_after;
end
nPos = (endPos - startPos) + 1;
for i =1:nPos
wtM(:, i) = wtM(:, i) * R(i);
end
Then put this line in their place:
wtM = bsxfun(#times,wtM,log2(nSymbols)./sum(wtM));
You will probably want to save the file under a new name, like seqlogo_norm.m, so you can still use the original unmodified SEQLOGO function. Now you can create sequence profile plots with all the columns normalized to the same height. For example:
S = {'LSGGQRQRVAIARALAL',... %# Sample amino acid sequence
'LSGGEKQRVAIARALMN',...
'LSGGQIQRVLLARALAA',...
'LSGGERRRLEIACVLAL',...
'FSGGEKKKNELWQMLAL',...
'LSGGERRRLEIACVLAL'};
seqlogo_norm(S,'alphabet','aa'); %# Use the modified SEQLOGO function
OLD ANSWER:
I'm not sure how to transform the sequence profile information to get the desired output from the Bioinformatics Toolbox function SEQLOGO, but I can show you how to modify the alternative seqlogo_new.m that I wrote for my answer to the related question you linked to. If you change the line that initializes bitValues from this:
bitValues = W{2};
to this:
bitValues = bsxfun(#rdivide,W{2},sum(W{2}));
Then you should get each column scaled to a height of 1. For example:
S = {'ATTATAGCAAACTA',... %# Sample sequence
'AACATGCCAAAGTA',...
'ATCATGCAAAAGGA'};
seqlogo_new(S); %# After applying the above modification

Answer 2

For now, my workaround is to generate a bunch of fake sequences that match the sequence profile, then feed those sequences to http://weblogo.berkeley.edu/logo.cgi . Here is the code to make the fake sequences:
function flatFakeSeqsFromPwm(pwm, letterOrder, nSeqsToGen, outFilename)
%translates a pwm into a bunch of fake seqs with the same probabilities
%for use with http://weblogo.berkeley.edu/
%pwm should be a 4xn or a 20xn position weight matrix. Each col must sum to 1
%letterOrder = e.g. 'ARNDCQEGHILKMFPSTWYV' for my data
%nSeqsToGen should be >= the # of pixels tall you plan to make your chart
[height windowWidth] = size(pwm);
assert(height == length(letterOrder));
assert(isequal(abs(1-sum(pwm)) < 1.0e-10, ones(1, windowWidth))); %assert all cols of pwm sum to 1.0
fd = fopen(outFilename, 'w');
for i = 0:nSeqsToGen-1
for seqPos = 1:windowWidth
acc = 0; %accumulator
idx = 0;
while i/nSeqsToGen >= acc
idx = idx + 1;
acc = acc + pwm(idx, seqPos);
end
fprintf(fd, '%s', letterOrder(idx));
end
fprintf(fd, '\n');
end
fclose(fd);
end