Question

I have a sequence call it ACGTCCT.... Is there anyway of plotting this without using stairs? Does anyone know how to make the colourful 2D/3D arrows towards the bottom of the page this: How to plot a gene graph for a DNA sequence say ATGCCGCTGCGC?

in matlab? Other suggestions on the ACGTCCT visualisation are welcome too.

Cheers

Answer 1

The arrow.m submission from FileExchange is what you need. It’s hard to imagine that it’s not built in, but at least this contribution fills the gap nicely. Here is an example using it like in that Q/A you linked to:

function randomWalk(seq)

n = length(seq);

ptStart = zeros(n, 3);
ptEnd   = zeros(n, 3);

cols = jet(n);

for i=1:n
    switch seq(i)
        case 'A'
            d = [1 0];
        case 'T'
            d = [-1 0];
        case 'G'
            d = [0 1];
        case 'C'
            d = [0 -1];
    end

    ptEnd(i,:) = ptStart(i,:) + [d 1];
    ptStart(i+1,:) = ptEnd(i,:);
end

rng = [min([ptStart; ptEnd], [], 1); max([ptStart; ptEnd], [], 1)];
axis(rng(:))
for i=1:n
    arrow(ptStart(i,:), ptEnd(i,:), 'BaseAngle', 90,...
                                    'TipAngle',  15,...
                                    'Length',    30,...
                                    'CrossDir', [1 1 0],...
                                    'EdgeColor', cols(i,:),...
                                    'FaceColor', cols(i,:));
end

axis equal
view([45 15])

>> randomWalk('ATGCGTCGTAACGT')