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barpatch.m
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function h = barpatch(data, varargin)
% BARPATCH Create bar graph with error bars using patch and line objects
%
% This function will create a grouped bar graph with error bars without
% using the standard plotting functions BAR and ERRORBAR. It uses PATCH to
% create the bars and LINE to construct the error bars.
%
% USAGE: h = barpatch(data, varargin)
% __________________________________________________________________________
% OUTPUT
% h: handles to all graphics objects
% __________________________________________________________________________
% INPUT
% data: data matrix to plot; rows are cases, cols are variables
% __________________________________________________________________________
% OPTIONAL INPUTS (VARARGIN)
% These are entered as `'name', value` argument pairs. Matching is not
% case-sensitive and partial name matches are OK. To see default values,
% run barpatch without any arguments.
%
% | Name | Description |
% | ----------- | --------------------------------------------------- |
% | figh | handle for figure to plot in |
% | newfig | flag to create and plot in a new figure |
% | groupidx | rows index columns of "data" to plot as a group |
% | groupname | labels for different groups of bars |
% | grouptick | flag to place tickmark between groups on x-axis |
% | groupspace | controls spacing between groups of bars |
% | barname | labels for different bars within groups (in legend) |
% | barcmap | colormap for distinguishing bars within a group |
% | barwidth, | width of bars (>1 produces overlapping bars) |
% | errlinewidth | width of error bar lines |
% | detachlegend | flag to plot legend in new figure (if applicable) |
% | t | figure title |
% | xl | x-axis label |
% | yl | y-axis label |
% | fontsize | base font size |
% | fontname | name of font to use |
% | fontunits | font units of finished product |
% | ytickformat | display formatting for yticklabels (e.g., '%.2f') |
% | yticklength | # of yticks (if empty, determined automatically) |
% | fontmultiplier1 | multiplier for next largest size from basefontsize |
% | fontmultiplier2 | multiplier for next largest size from basefontsize |
% | fontmultiplier3 | multiplier for next largest size from basefontsize |
%
% __________________________________________________________________________
% USAGE EXAMPLE
% data = randn(10, 8);
% groupidx = [1 2; 3 4; 5 6; 7 8];
% groupn = {'Group A' 'Group B' 'Group C' 'Group D'};
% xl = 'X-Axis Label';
% yl = 'Y-Axis Label';
% t = 'The Figure Title';
% h = barpatch(data, 'groupidx', groupidx, 'groupname', groupn, 'xl', xl, 'yl', yl, 't', t);
%
% ---------------------- Copyright (C) 2014 Bob Spunt ----------------------
% Created: 2015-03-09
% Email: [email protected]
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or (at
% your option) any later version.
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see: http://www.gnu.org/licenses/.
% __________________________________________________________________________
def = { ...
'newfig', 1, ...
'groupidx', [], ...
'groupname', [], ...
'grouptick', 0, ...
'groupspace' 0.5, ...
'barname', [], ...
'barcmap', 'gray', ...
'mapminmax', [.025 .975], ...
'barwidth', .95, ...
'detachlegend', 0, ...
'errlinewidth', 1.5, ...
'xl', [], ...
'yl', [], ...
't', [], ...
'fontunits', 'norm', ...
'fontsize', 12, ...
'fontmultiplier1', 1.2, ...
'fontmultiplier2', 1.4, ...
'fontmultiplier3', 1.6, ...
'fontname', 'Arial', ...
'ytickformat', '%.2f', ...
'yticklength', [] ...
};
% | Check Varargin
% | ========================================================================
vals = setargs(def, varargin);
if nargin<1, mfile_showhelp; fprintf('\t| - VARARGIN DEFAULTS - |\n'); disp(vals); return; end
nvar = size(data, 2);
if isempty(groupidx), groupidx = 1:nvar; end
if any(size(groupidx)==1), ngroup = 1; else ngroup = size(groupidx, 1); end
% | Compute means, ses, etc.
% | ========================================================================
nbar = nvar/ngroup;
allm = nanmean(data);
allse = nansem(data);
% | Check Validity of Arguments
% | ========================================================================
if ~isempty(barname) && length(barname)~=nbar, error('Length of "barname" must match group size'); end
if and(~isempty(groupname), ischar(groupname)), groupname = cellstr(groupname); end
if and(~isempty(groupname), length(groupname)~=ngroup), error('Length of "groupname" must match number of groups'); end
if numel(groupidx)~=nvar, error('Number of indices in "groupidx" does not match number of columns in input "data"'); end
% | Grab or Make Figure
% | ========================================================================
if newfig
h.fig = figure('color','white');
h.ax = gca;
set(h.ax, 'position', [.075 .125 .875 .825]);
else
h.fig = gcf;
h.ax = gca;
end
set(findall(h.fig, '-property', 'units'), 'units', 'norm');
set(h.ax, 'FontSize', fontsize); % base font size
propfs = round(get(h.ax, 'FontSize')*fontmultiplier1); % font size proportioned wrt to axis fontsize
set(gca, 'xticklabel', []);
% | Check Color Map
% | ========================================================================
if ischar(barcmap)
map = quantile(colormap(barcmap), min(mapminmax):(range(mapminmax)+.01)/nbar:max(mapminmax));
elseif isnumeric(barcmap)
mapdim = size(barcmap);
if any([mapdim(1)<nbar mapdim(2)~=3])
error('You have specified an invalid colormap in input "barcmap"');
end
if mapdim(1)>nbar
fprintf('\n- WARNING: Using just the first %d rows of the input colormap - \n\n', nbar);
end
map = barcmap(1:nbar,:);
end
% | Create the Pretty Patch of Bars with Lines, Labels, Tigers, Bears, etc.
% | ========================================================================
h.patch = zeros(ngroup, nbar);
h.error = zeros(ngroup, nbar);
h.cap = zeros(ngroup, nbar);
xcenter = .25+.5:1:nbar;
if ngroup > 1
xcenter = repmat(xcenter, ngroup, 1);
gwidth = repmat(nbar + groupspace, ngroup, 1);
xcenter(2:end,:) = xcenter(2:end,:) + repmat(cumsum(gwidth(2:end)), 1, nbar);
tickcenter = xcenter(:,end) + .50 + .25;
gcenter = sum(xcenter(:,[1 end]), 2)/2;
fcenter = sum(gcenter)/ngroup;
else
gcenter = sum(xcenter)/nbar;
fcenter = sum(xcenter)/nbar;
end
halfbar = barwidth/2;
xc = [xcenter-halfbar xcenter+halfbar xcenter+halfbar xcenter-halfbar];
for g = 1:ngroup
m = allm(groupidx(g,:));
se = allse(groupidx(g,:));
for i = 1:nbar
xcoord = xc(g,i:nbar:end);
ycoord = [0 0 m(i) m(i)];
h.patch(g,i) = patch(xcoord, ycoord, map(i,:), 'linestyle', 'none', 'edgecolor', map(end,:));
hold on
% - ERROR BAR
if m(i) < 0
ylim = [m(i)-se(i) m(i)];
ycap = ylim(1);
else
ylim = [m(i) m(i) + se(i)];
ycap = ylim(2);
end
h.error(g,i) = line([xcenter(g,i) xcenter(g,i)], ylim); % line
h.cap(g,i) = line([xcenter(g,i)-.05 xcenter(g,i)+.05], [ycap ycap]); % horizontal cap
set(h.error(g,i), 'color', get(h.ax, 'ycolor'), 'linewidth', errlinewidth);
set(h.cap(g,i), 'color', get(h.ax, 'ycolor'), 'linewidth', errlinewidth);
% set(h.error(g,i), 'color', get(h.ax, 'ycolor'), 'linewidth', get(h.patch(g,i), 'linewidth'));
% set(h.cap(g,i), 'color', get(h.ax, 'ycolor'), 'linewidth', get(h.patch(g,i), 'linewidth'));
hold on
end
end
set(h.ax, 'units', 'normal');
% | Make legend
% | ========================================================================
if ~isempty(barname)
if detachlegend
h.legend = legendfree(barname, 'fontsize', ceil(propfs*fontmultiplier1), 'cmap', map);
% set(h.ax, 'units', 'pix');
% refpos = get(h.ax, 'position');
% set(h.ax, 'units', 'norm');
% multiplier = 1/6;
% legh = (refpos(4)*multiplier)*nbar;
% legpos = [1 1 legh*2 legh];
% h.leg = figure('color','white', 'units', 'pix', 'pos', legpos);
% h.legax = gca;
% w = .9*(1/nbar);
% ybottom = ((1/nbar)-w)/2:(1/nbar):1;
% ytop = ybottom + w;
% xleft = ((1/nbar)-w)/2;
% xright = xleft + w;
% ycoord = [ybottom' ybottom' ytop' ytop'];
% xcoord = [xleft' xright' xright' xleft'];
% ycoord = sortrows(ycoord, -1);
% for i = 1:length(barname)
% p(i) = patch(xcoord, ycoord(i,:), map(i,:), 'linestyle', 'none', 'edgecolor', map(end,:));
% end
% set(h.legax, 'ylim', [0 1], 'xlim', [0 2]);
% axis off;
% labx = (1/nbar) + xleft;
% laby = ((1/nbar)/2):(1/nbar):1;
% laby = sort(laby, 2, 'descend');
% for g = 1:nbar
% h.leglabel(g) = text(labx, laby(g), barname{g}, 'margin', 1, 'horizontalalign', 'left', 'verticalalign', 'middle', 'FontSize', ceil(propfs*fontmultiplier1));
% end
axes(h.ax);
else
h.leg = legend(h.patch(1,:), barname);
set(h.leg, ...
'Location', 'Best', ...
'FontWeight', 'normal', ...
'FontSize', ceil(propfs*fontmultiplier2), ...
'EdgeColor', get(gca, 'color'));
hold on
end
end
% | LINE FOR X-AXIS (BASELINE)
% | ========================================================================
h.xline = line(get(h.ax, 'xlim'), [0 0]);
set(h.xline, 'Color', get(h.ax, 'ycolor'), 'LineWidth', get(h.ax, 'linewidth'));
set(h.ax, 'xcolor', get(gca, 'color'));
% | GROUP DIVIDING TICK MARK
% | ========================================================================
if and(ngroup>1, grouptick)
tln = .025*range(get(h.ax, 'ylim'));
for g = 1:ngroup-1
h.xtick(g) = line([tickcenter(g) tickcenter(g)], [-tln tln]);
set(h.xtick(g), 'Color', get(h.ax, 'ycolor'), 'LineWidth', get(h.ax, 'linewidth'));
end
end
% | GROUP LABEL
% | ========================================================================
if ~isempty(groupname)
h.grouplabel = zeros(ngroup);
barlim = cell2mat(get(h.patch, 'ydata'));
errlim = cell2mat(get(h.error, 'ydata'));
alllim = [barlim(:); errlim(:)];
alllim = [min(alllim(:)) max(alllim(:))];
for g = 1:ngroup
h.grouplabel(g) = text(0, alllim(1), groupname{g}, 'margin', 1, 'horizontalalign', 'center', 'FontSize', ceil(propfs*fontmultiplier1));
set(h.grouplabel(g), 'position', [gcenter(g,1) alllim(1)], 'verticalalign', 'top', 'tag', 'groupname', 'horizontalalign', 'center');
end
ext = get(h.grouplabel(1), 'extent');
ylim = get(h.ax, 'ylim');
ylim(1) = ext(2);
set(h.ax, 'ylim', ylim);
end
% | X-LABEL
% | ========================================================================
if ~isempty(xl)
ylim = get(h.ax, 'ylim');
if ~isempty(groupname), ylim(1) = ylim(1) - (range(ylim)*.05); end
h.xlabel = text(fcenter, ylim(1), xl, ...
'margin', 1, ...
'FontSize', ceil(propfs*fontmultiplier2), ...
'horizontalalign', 'center', ...
'verticalalign', 'top', ...
'tag', 'xlabel' ...
);
ext = get(h.xlabel, 'extent');
ylim = get(h.ax, 'ylim');
ylim(1) = ext(2);
set(h.ax, 'ylim', ylim);
end
% | Y-LABEL
% | ========================================================================
if ~isempty(yl)
h.ylabel = ylabel(yl, 'FontSize', ceil(propfs*fontmultiplier1), 'FontWeight', 'normal');
end
% | TITLE
% | ========================================================================
if ~isempty(t)
barlim = cell2mat(get(h.patch, 'ydata'));
errlim = cell2mat(get(h.error, 'ydata'));
alllim = [barlim(:); errlim(:)];
alllim = [min(alllim(:)) max(alllim(:))];
h.title = text(fcenter, alllim(2)+(.025*range(alllim)), t, ...
'margin', 1, ...
'FontSize', ceil(propfs*fontmultiplier3), ...
'horizontalalign', 'center', ...
'verticalalign', 'bottom', ...
'tag', 'title' ...
);
ext = get(h.title(1), 'extent');
ylim = get(h.ax, 'ylim');
ylim(2) = sum(ext([2 4]));
set(h.ax, 'ylim', ylim);
end
% | FORMAT TICKLABELS
% | ========================================================================
% if yticklength
% ylim = get(h.ax, 'ylim');
% set(h.ax, 'ytick', linspace(ylim(1), ylim(2), yticklength));
% end
% if and(~isempty(ytickformat), ~isempty(get(h.ax, 'yticklabel')))
% yt = get(h.ax, 'ytick');
% yts = cell(size(yt));
% for i = 1:length(yt)
% yts{i} = sprintf(ytickformat, yt(i));
% end
% set(h.ax, 'yticklabel', yts);
% end
% | FINAL CLEANUP, PROPERTY SETTING
% | ========================================================================
set(findall(h.fig, '-property', 'FontName'), 'FontName', fontname, 'FontUnits', 'norm');
set(findall(h.fig, '-property', 'units'), 'units', fontunits);
if newfig, set(h.ax, 'OuterPosition', [0 0 1 1]); end
end
% ==========================================================================
%
% ------------------------------ SUBFUNCTIONS ------------------------------
%
% ==========================================================================
function argstruct = setargs(defaultargs, varargs)
% SETARGS Name/value parsing and assignment of varargin with default values
%
% This is a utility for setting the value of optional arguments to a
% function. The first argument is required and should be a cell array of
% "name, default value" pairs for all optional arguments. The second
% argument is optional and should be a cell array of "name, custom value"
% pairs for at least one of the optional arguments.
%
% USAGE: argstruct = setargs(defaultargs, varargs)
% __________________________________________________________________________
% OUTPUT
%
% ARGSTRUCT
% structure containing the final argument values
% __________________________________________________________________________
% INPUTS
%
% DEFAULTARGS
% cell array of "'Name', value" pairs for all variables with default
% values
%
% VARARGS [optional]
% cell array of user-specified "'Name', value" pairs for one or more of
% the variables with default values. this will typically be the
% "varargin" cell array. for each pair, SETARGS determines if the
% specified variable name can be uniquely matched to one of the default
% variable names specified in DEFAULTARGS. matching uses STRNCMPI and
% thus is case-insensitive and open to partial name matches (e.g.,
% default variable name 'FontWeight' would be matched by 'fontweight',
% 'Fontw', etc.). if a match is found, the user-specified value is then
% used in place of the default value. if no match is found or if
% multiple matches are found, SETARGS returns an error and displays in
% the command window information about the argument that caused the
% problem.
% __________________________________________________________________________
% USAGE EXAMPLE (TO BE USED AT TOP OF FUNCTION WITH VARARGIN)
%
% defaultargs = {'arg1', 0, 'arg2', 'words', 'arg3', rand};
% argstruct = setargs(defaultargs, varargin)
%
% ---------------------- Copyright (C) 2015 Bob Spunt -----------------------
% Created: 2015-03-11
% Email: [email protected]
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or (at
% your option) any later version.
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see: http://www.gnu.org/licenses/.
%
if nargin < 1, mfile_showhelp; return; end
if nargin < 2, varargs = []; end
defaultargs = reshape(defaultargs, 2, length(defaultargs)/2)';
if ~isempty(varargs)
if mod(length(varargs), 2)
error('Optional inputs must be entered as "''Name'', Value" pairs, e.g., myfunction(''arg1'', val1, ''arg2'', val2)');
end
arg = reshape(varargs, 2, length(varargs)/2)';
for i = 1:size(arg,1)
idx = strncmpi(defaultargs(:,1), arg{i,1}, length(arg{i,1}));
if sum(idx) > 1
error(['Input "%s" matches multiple valid inputs:' repmat(' %s', 1, sum(idx))], arg{i,1}, defaultargs{idx, 1});
elseif ~any(idx)
error('Input "%s" does not match a valid input.', arg{i,1});
else
defaultargs{idx,2} = arg{i,2};
end
end
end
for i = 1:size(defaultargs,1), assignin('caller', defaultargs{i,1}, defaultargs{i,2}); end
if nargout>0, argstruct = cell2struct(defaultargs(:,2), defaultargs(:,1)); end
end
function mfile_showhelp(varargin)
% MFILE_SHOWHELP
ST = dbstack('-completenames');
if isempty(ST), fprintf('\nYou must call this within a function\n\n'); return; end
eval(sprintf('help %s', ST(2).file));
end
function h = legendfree(labels, varargin)
% LEGENDFREE
%
% ---------------------- Copyright (C) 2014 Bob Spunt ----------------------
% Created: 2015-03-09
% Email: [email protected]
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or (at
% your option) any later version.
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see: http://www.gnu.org/licenses/.
% __________________________________________________________________________
def = { ...
'titlestr', '', ...
'cmap', 'gray', ...
'fontsize', 10, ...
'fontname', 'Arial', ...
};
% | Check Varargin
% | ========================================================================
vals = setargs(def, varargin);
if nargin<1, mfile_showhelp; fprintf('\t| - VARARGIN DEFAULTS - |\n'); disp(vals); return; end
% | Check Color Map
% | ========================================================================
nlabel = length(labels);
if ischar(cmap)
map = quantile(colormap(cmap), .1:.801/nlabel:.90);
elseif isnumeric(cmap)
mapdim = size(cmap);
if any([mapdim(1)<nlabel mapdim(2)~=3])
error('You have specified an invalid cmap in input "cmap"');
end
if mapdim(1)>nlabel
fprintf('\n- WARNING: Using just the first %d rows of the input cmap - \n\n', nlabel);
end
map = cmap(1:nlabel,:);
end
% | Estimate Size
% | ========================================================================
[strw,strh] = strsize(labels, 'fontsize', fontsize, 'fontname', fontname);
ht = (max(strh)*1.25)*nlabel;
wd = max(strw)*1.25 + (max(strh)*1.25);
figrat = wd/ht;
% | DO IT
% | ========================================================================
h.legfig = figure('color', 'white', 'ToolBar', 'none', 'menubar', 'none', 'units', 'pixel', 'pos', [10 10 wd ht]);
set(h.legfig, 'units', 'norm');
h.legax = axes(h.legfig, 'units', 'norm', 'pos', [0.01 0.01 .98 .98]);
w = .9*(1/nlabel);
ybottom = ((1/nlabel)-w)/2:(1/nlabel):1;
ytop = ybottom + w;
xleft = ((1/nlabel)-w)/2;
xright = xleft + w;
ycoord = [ybottom' ybottom' ytop' ytop'];
xcoord = [xleft' xright' xright' xleft'];
ycoord = sortrows(ycoord, -1);
for i = 1:length(labels)
h.patch(i) = patch(xcoord, ycoord(i,:), map(i,:), 'linestyle', 'none', 'edgecolor', map(end,:));
end
axis off;
set(h.legax, 'ylim', [0 1], 'xlim', [0 figrat], 'units', 'pixels');
labx = (1/nlabel) + xleft;
laby = ((1/nlabel)/2):(1/nlabel):1;
laby = sort(laby, 2, 'descend');
for g = 1:nlabel
h.leglabel(g) = text(labx, laby(g), labels{g}, 'margin', 1, 'horizontalalign', 'left', 'verticalalign', 'middle', 'FontSize', fontsize);
end
% | FINAL CLEANUP, PROPERTY SETTING
% | ========================================================================
set(findall(h.legfig, '-property', 'FontName'), 'FontName', fontname, 'FontUnits', 'norm');
set(findall(h.legfig, '-property', 'units'), 'Units', 'pixels');
if ~isempty(titlestr)
figpos = get(h.legfig, 'pos');
tith = max(strh)*1.5;
figpos(4) = figpos(4) + tith;
set(h.legfig, 'pos', figpos);
axpos = get(h.legax, 'pos');
h.title = text(axpos(1), sum(axpos([2 4])), titlestr, ...
'units', 'pixel', ...
'margin', 1, ...
'horizontalalign', 'left', ...
'verticalalign', 'bottom', ...
'fontweight', 'bold', ...
'fontname', fontname, ...
'FontSize', fontsize*1.1);
end
end
function [strw, strh] = strsize(string, varargin)
% STRSIZE Calculate size of string
%
% USAGE: strsize(string, varargin)
%
% ---------------------- Copyright (C) 2015 Bob Spunt ----------------------
% Created: 2015-07-14
% Email: [email protected]
% __________________________________________________________________________
def = { ...
'FontSize', get(0, 'DefaultTextFontSize'), ...
'FontName', get(0, 'DefaultTextFontname'), ...
'FontWeight', get(0, 'DefaultTextFontWeight'), ...
'FontAngle', get(0, 'DefaultTextFontAngle'), ...
'FontUnits', get(0, 'DefaultTextFontUnits') ...
};
vals = setargs(def, varargin);
if nargin==0, mfile_showhelp; fprintf('\t| - VARARGIN DEFAULTS - |\n'); disp(vals); return; end
if ischar(string), string = cellstr(string); end
nstr = length(string);
strw = zeros(nstr, 1);
strh = zeros(nstr, 1);
tmpfig = figure('visible', 'off');
for i = 1:nstr
hTest = text(1,1, string{i}, 'Units','Pixels', 'FontUnits',FontUnits,...
'FontAngle',FontAngle,'FontName',FontName,'FontSize',FontSize,...
'FontWeight',FontWeight,'Parent',gca, 'Visible', 'off');
textExt = get(hTest,'Extent');
strh(i) = textExt(4);
strw(i) = textExt(3);
delete(hTest);
end
delete(tmpfig);
% | If using a proportional font, shrink text width by a fudge factor to account for kerning.
if ~strcmpi(FontName, 'Fixed-Width'), strw = strw*0.9; end
end