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glyvis.m
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glyvis.m
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function glyvis(mspos,bondmap,linkage,bondescription,mspara,directionseq,identity,options)
% GLYVIS: Glycan visualizer is the main function for displaying glycans
%
% Syntax:
% glyvis(mspos,bondmap,linkage,bondbreak,mspara,directionseq,identity,options)
%
% Input:
% mspos: n x 2 numerical array, the monosaccharide position in glycan
% bondmap: m x m numerical array, the map showing connection between
% monosaccharides.
% linkage: n x 1 cell array of strings, the glycosidic bond information.
% bondbreak: 1 x 3 cell array, 1st element contains marker position, 2nd
% position the type, 3rd the content.
% mspara: structure, the shape, color size, perimeter width and monosac.
% name of the monosac. to be drawn.
% directionseq: 1 x n numerical array, the orientation of monosac. symbols
% identity: the nature of each symbol, can be SHAPE, ANOMER or CHAR
% options: global drawing options
%
% Output:
% N/A
%
% Note:
% N/A
%
% Example:
% N/A. Set breakpoints in main program.
%
% Children function:
% DRAWSHAPES
%
%
% DrawGlycan authors: Kai Cheng, Yusen Zhou, Sriram Neelamegham
%(c) 2019, Research Foundation for State University of New York. All rights reserved
%
identityseq = cell(size(mspos,1),1);
identityseq(:) = {'SHAPE'};
fig = options.figurehandle;
if ~isempty(identity)
identityinfo = cell2mat(identity);
identityseq(identityinfo(identityinfo(:,1) == 1,2)) = deal({'CHAR'});
identityseq(identityinfo(identityinfo(:,1) == 2,2)) = deal({'ANOMER'});
end
paintlink(mspos,bondmap,bondescription,options)
if ~isempty(bondescription)
bondbreakpos = cell2mat(bondescription(:,1));
bondbreaktyp = bondescription(:,2);
bondbreakinfo = bondescription(:,3);
else
bondbreakpos = [];
bondbreaktyp = '';
bondbreakinfo = '';
end
if ischar(bondbreakinfo)
bondbreakinfo = {bondbreakinfo};
end
if ismember(lower(options.orientation),{'right','down'})
alignment = {'left','right'};
elseif ismember(lower(options.orientation),{'left','up'})
alignment = {'right','left'};
end
if strcmpi(options.orientation,'left') || strcmpi(options.orientation,'right')
msaddtextrot = 0;
elseif strcmpi(options.orientation,'up') || strcmpi(options.orientation,'down')
msaddtextrot = 90;
end
for i = 1:size(mspos,1)
linkdist = mspara.size(i)/2*(1+options.linkinfodist); % distance: outer rim + 20% radius (default)
drawshapes(mspara.shape{i},mspos(i,:),mspara.size(i),mspara.color{i},...
mspara.periwidth(i),directionseq(i),mspara.name{i},identityseq{i},options);
if strcmpi(mspara.shape{i},'flat hexagon') && strcmpi(mspara.color{i},'White') && ...
strcmpi(identityseq{i},'SHAPE') && ~strcmpi(mspara.name{i},'unknown')
text(fig,mspos(i,1),mspos(i,2),mspara.name{i}(1),'fontsize',options.fontsize*1.5,...
'horizontalalignment','center');
end
end
for i = 1:size(mspos,1)
linktyp = linkage{i}(1);
if strcmpi(linktyp,'a')
linktyp = 945;
% linktyp = '\alpha';
elseif strcmpi(linktyp,'b')
linktyp = 946;
% linktyp = '\beta';
elseif strcmpi(linktyp,'?')
linktyp = '';
end
linknum = regexp(linkage{i}(2:end),'-[?\d/\\]+','match');
linknum = linknum{1}(2:end);
if strcmpi(linknum,'?')
linknum = '';
end
if i == 1
if strcmpi(options.orientation,'left')
lastmonosac = mspos(1,:) + [1,0];
elseif strcmpi(options.orientation,'right')
lastmonosac = mspos(1,:) - [1,0];
elseif strcmpi(options.orientation,'up')
lastmonosac = mspos(1,:) - [0,1];
elseif strcmpi(options.orientation,'down')
lastmonosac = mspos(1,:) + [0,1];
end
else
lastmonosac = mspos(find(bondmap(:,i),1,'first'),:);
end
if mspos(i,1)-lastmonosac(1) ~= 0
alpha = atan((mspos(i,2)-lastmonosac(2))/(mspos(i,1)-lastmonosac(1)));
else
alpha = pi/2;
end
xdif = mspos(i,1)-lastmonosac(1);
ydif = mspos(i,2)-lastmonosac(2);
msdistance = sqrt(xdif^2+ydif^2);
if xdif > 0 && ydif <= 0
alpha = alpha + 2*pi;
elseif xdif <= 0 && ydif < 0
alpha = alpha + pi;
elseif xdif < 0 && ydif >= 0
alpha = alpha + pi;
end % fix alpha value
typx = mspos(i,1) - linkdist * cos(alpha - options.linkinfotheta/180*pi);
typy = mspos(i,2) - linkdist * sin(alpha - options.linkinfotheta/180*pi);
numx = lastmonosac(1) + linkdist * cos(alpha + options.linkinfotheta/180*pi);
numy = lastmonosac(2) + linkdist * sin(alpha + options.linkinfotheta/180*pi);
if strcmpi(options.showlink,'yes')
text(fig,typx,typy,char(double(linktyp)),'fontsize',options.linkfontsize,'horizontalalignment','center');
text(fig,numx,numy,char(double(linknum)),'fontsize',options.linkfontsize,'horizontalalignment','center');
end
whichbondbreak = ismember(bondbreakpos,i);
if any(whichbondbreak)
breakpos = bondbreakpos(whichbondbreak);
breaktype = bondbreaktyp(whichbondbreak);
breakinfo = bondbreakinfo(whichbondbreak);
centx = mean([lastmonosac(1),mspos(i,1)]);
centy = mean([lastmonosac(2),mspos(i,2)]);
linestart = [centx + options.bondbreaksiglength/1.4 * cos(alpha + pi/2),...
centy + options.bondbreaksiglength/1.4 * sin(alpha + pi/2)];
lineend = [centx - options.bondbreaksiglength/1.4 * cos(alpha + pi/2),...
centy - options.bondbreaksiglength/1.4 * sin(alpha + pi/2)];
for j = 1:numel(breakpos)
typelinefix = [options.bondbreaksiglength/ 5 * cos( 0 /180*pi+alpha),...
options.bondbreaksiglength/ 5 * sin( 0 /180*pi+alpha)];
typetextfix = [options.bondbreaksiglength/ 5 * cos( 90 /180*pi+alpha),...
options.bondbreaksiglength/ 5 * sin( 90 /180*pi+alpha)];
if strcmpi(breaktype{j},'NR')
typelineend = linestart + typelinefix;
plot(fig,[typelineend(1),linestart(1)],[typelineend(2),linestart(2)],'k');
text(fig,typelineend(1)+ typetextfix(1),typelineend(2)+ typetextfix(2),...
char(double(breakinfo{j})),'horizontalalignment',alignment{1},...
'fontsize',options.fontsize);
plot(fig,[linestart(1),lineend(1)],[linestart(2),lineend(2)],'k');
elseif strcmpi(breaktype{j},'R')
typelineend = lineend - typelinefix;
plot(fig,[typelineend(1),lineend(1)],[typelineend(2),lineend(2)],'k');
text(fig,typelineend(1)- typetextfix(1),typelineend(2)- typetextfix(2),...
char(double(breakinfo{j})),'horizontalalignment',alignment{2},...
'fontsize',options.fontsize);
plot(fig,[linestart(1),lineend(1)],[linestart(2),lineend(2)],'k');
elseif strcmpi(breaktype{j},'U')
if msaddtextrot % vertical glycan
text(fig,mspos(i,1) - options.monosacsize*1.02/2,mspos(i,2),...
char(double(breakinfo{j})),'horizontalalignment','center',...
'verticalalignment','middle','fontsize',options.fontsize * 1.25);
else % horizontal glycan
text(fig,mspos(i,1),mspos(i,2) + options.monosacsize*1.02/2,char(double(breakinfo{j})),...
'horizontalalignment','center',...
'verticalalignment','bottom','fontsize',options.fontsize * 1.25);
end
elseif strcmpi(breaktype{j},'D')
if msaddtextrot % vertical glycan
text(fig,mspos(i,1) + options.monosacsize*1.02/2,mspos(i,2),char(double(breakinfo{j})),...
'horizontalalignment','center',...
'verticalalignment','middle','fontsize',options.fontsize * 1.25);
else % horizontal glycan
text(fig,mspos(i,1),mspos(i,2) - options.monosacsize*1.02/2,char(double(breakinfo{j})),...
'horizontalalignment','center',...
'verticalalignment','top','fontsize',options.fontsize * 1.25);
end
elseif strcmpi(breaktype{j},'C')
if ismember(breakinfo{j},{'f','p','o'})
fontangle = 'italic';
else
fontangle = 'normal';
end
text(fig,mspos(i,1),mspos(i,2),char(double(breakinfo{j})),'horizontalalignment','center',...
'verticalalignment','middle',...
'fontsize',options.fontsize * 1.25,'FontAngle',fontangle);
end
end
end
end
end