fix some aspect of formatting for matlab plots according to J Neurosci guidelines

jneurosci.m

function [ fHandle ] = jneurosci(fHandle, colWidth)
%jneurosci - provide some defaults for figures to get to JNeurosci style
%
%      usage: [ fHandle ] = jneurosci( fHandle )
%         by: lpzds1
%       date: May 28, 2015
%
%     inputs: fHandle, colWidth [1, 1.5, 2]
%    outputs: fHandle
%
%    purpose: set font style, size, tight crop, paper size, etc.
%             appropriate for a jneurosci figure
%
%        e.g: % make a figure with 4 subplot
%             for ii = 1:4, subplot(2,2,ii), plot(sin(linspace(0,2*pi,100))), title(sprintf('figure %i', ii)), xlabel('bla'), ylabel('blabla'), end
%             jneurosci(gcf, 1.5) % convert to 1.5 column format.
%             saveas(gcf, 'test.pdf')

if nargin < 2 || ~any( colWidth == [1 1.5 2])
    colWidth = 1; 
    fprintf('setting column width to: %.1f\n', colWidth);
end

if nargin < 1 || ~ishandle(fHandle)
    disp('(uhoh) provide a valid figure handle, please')
    return
end

if ~(exist('tightfig','file') == 2)
    disp('(uhoh) you need tightfig.m to use this function')
    web('http://www.mathworks.com/matlabcentral/fileexchange/34055-tightfig')
    return
end

% column is: 

% Figures must be submitted at the size they are to appear in The Journal
% of Neuroscience. They should be the smallest size that will convey the
% essential scientific information, and sized to 1 column (maximum width
% 8.5 cm), 1.5 columns (maximum width 11.6 cm) or 2 columns (maximum width
% 17.6 cm).         

% tightfig introduces a tiny border around... so need to account for that.
switch colWidth 
    case 1
        paperWidth = 8.5 - 0.15;
    case 1.5
        paperWidth = 11.6 - 0.15;
    case 2
        paperWidth = 17.6 - 0.15;
end


%# set size on printed paper
%# WYSIWYG mode: you need to adjust your screen's DPI (*)
set(fHandle, 'Units', 'centimeters')
figureDims = get(fHandle, 'Position');

% don't let matlab change ticks
set(findall(fHandle,'type','axes'), ...
    'xtickmode','manual', ...
    'ytickmode','manual')

% resize to make w equal the currentPaperPosition(3)
marginOffset = [0 0];
aspectRatio = figureDims(3) ./ figureDims(4);
newPaperPosition = [marginOffset([1 2]), paperWidth, paperWidth./aspectRatio];
set(fHandle, 'Position', [5 5 newPaperPosition([3 4])]); % on screen, away from bottom left.
set(fHandle, 'PaperPosition', newPaperPosition);
set(fHandle, 'PaperType', 'a4');

% defaults - could also pass those in?!
% text and other stuff...
f.text.fontsize = 8;
f.text.fontname = 'Helvetica';
f.text.fontangle = 'normal';
f.text.fontunits = 'points';

% tick labels
f.axis.fontsize = 7;
f.axis.fontname = 'Helvetica';
f.axis.fontangle = 'normal';
f.axis.fontunits = 'points';

% change size of figure to appropriate paper size, then call tightfig!
% this is to make sure the final figure has the right dimensions:

% axis
set(findall(fHandle,'type','axes'),...
    'fontangle',f.axis.fontangle, ...
    'fontsize',f.axis.fontsize, ...
    'fontname',f.axis.fontname, ...
    'fontunits',f.axis.fontunits);

% text
set(findall(fHandle,'type','text'),...
    'fontangle',f.text.fontangle, ...
    'fontsize',f.text.fontsize, ...
    'fontname',f.text.fontname, ...
    'fontunits',f.text.fontunits);


% now call tightfig to remove white space before exporting
fHandle = tightfig(fHandle);

end