Multiple y axes in MATLAB (axis alignment issue when printing)

Question

Here is a sample of a strange problem. I'd like to plot curves with multiple y axes and I use a fairly common method in MATLAB.

function plot_test()

clear; 
savefile = 1;

scrsz = get(0,'ScreenSize');
figure('Position',[1 1 0.9 * scrsz(3) 0.9 * scrsz(4)]);

hold on;
box on;

x = 0:1:10;

h1 = plot(x, x.^2 , 'r', 'LineWidth', 2.5);

%Axis label
xlabel('XLabel', 'FontSize', 20, 'Interpreter', 'latex');
ylabel('YLabel', 'FontSize', 20, 'Interpreter', 'latex');
set(gca, 'FontSize', 20, 'LineWidth', 3);

ax1 = gca;
ax2 = axes('Position',get(ax1,'Position'),'XAxisLocation','top','YAxisLocation','right','Color','none','XColor','none','YColor','k');
linkaxes([ax1 ax2],'x');
hold on
box on;
h2 = plot(x, x, 'b', 'Parent', ax2, 'LineWidth', 2.5);
ylabel('Second YLabel', 'FontSize', 20, 'Interpreter', 'latex');
set(gca, 'FontSize', 20, 'LineWidth', 3);

hl=legend([h1 h2],{'First Line','Second Line'});
set(hl,'FontSize',15,'Location','Northwest', 'Orientation','Vertical')


%Save pdf
if savefile
    % Backup previous settings
    prePaperType = get(gcf,'PaperType');
    prePaperUnits = get(gcf,'PaperUnits');
    preUnits = get(gcf,'Units');
    prePaperPosition = get(gcf,'PaperPosition');
    prePaperSize = get(gcf,'PaperSize');

    % Make changing paper type possible
    set(gcf,'PaperType','<custom>');

    % Set units to all be the same
    set(gcf,'PaperUnits','inches');
    set(gcf,'Units','inches');


    % Save the pdf
    print -dpdf Test.pdf;

    % Restore the previous settings
    set(gcf,'PaperType',prePaperType);
    set(gcf,'PaperUnits',prePaperUnits);
    set(gcf,'Units',preUnits);
    set(gcf,'PaperPosition',prePaperPosition);
    set(gcf,'PaperSize',prePaperSize);    
end

The objective is to print a PDF of the figure and save it in the same folder as Test.pdf. This is accomplished but the axes are misaligned. On my Windows machine it looks horrible while on a Mac it looks almost okay (but if you look closely, the y-axes are indeed misaligned at the bottom).

This only happens when I use a second axis. Without that, all this runs perfectly. Any idea why?

http://stackoverflow.com/questions/30524322/matlab-add-additional-y-axis-linearly-scaled-to-original-and-print-to-pdf-w?rq=1 - I think this may be a common "error"... — 16per9, Apr 19 '16 at 08:28
Why don't instead of saving directly a pdf file, why don't you save an *.eps file and then convert it to pdf? It's a workaround of course but give it a try — 16per9, Apr 19 '16 at 08:29
@16per9 sure, I'm manually saving it as a .png and then using it for now. I'm not sure if there's an automated way to save as png and then convert to pdf in MATLAB though and that's what I'm after (the end user should be able to get output pdfs in one click) — user1936752, Apr 19 '16 at 08:39
http://www.mathworks.com/help/matlab/ref/print.html - this allows you to save your figure directly. Not sure about the pdf conversion — 16per9, Apr 19 '16 at 08:44

score 0 · Accepted Answer · answered Apr 21 '16 at 10:25

Okay, so I found a way: The trick is to use plotyy. Sample code below

function plot_test2()

clear; 
savefile = 1;

scrsz = get(0,'ScreenSize');
figure('Position',[1 1 0.9 * scrsz(3) 0.9 * scrsz(4)]);

hold on;
box on;

x=(0:1:10);
y1=x;
y2=x.^2;
[hAx, hLine1, hLine2] = plotyy(x,y1,x,y2);


%Axis label
xlabel(hAx(1),'XLabel', 'FontSize', 20, 'Interpreter', 'latex', 'Color', 'k');
ylabel(hAx(1),'YLabel', 'FontSize', 20, 'Interpreter', 'latex', 'Color', 'k');
ylabel(hAx(2),'Second YLabel', 'FontSize', 20, 'Interpreter', 'latex');

set(hAx,{'ycolor'},{'k';'k'})
set(hAx,{'FontSize'},{20;20}, {'LineWidth'}, {3;3})
set(hLine1,'LineWidth', 3)
set(hLine2,'LineWidth', 3)
set(hLine1,'Color', 'r')
set(hLine2,'Color', 'b')

hl=legend([hLine1 hLine2],{'First Line','Second Line'});
set(hl,'FontSize',15,'Location','Northwest', 'Orientation','Vertical')


%Save pdf
if savefile
    % Backup previous settings
    prePaperType = get(gcf,'PaperType');
    prePaperUnits = get(gcf,'PaperUnits');
    preUnits = get(gcf,'Units');
    prePaperPosition = get(gcf,'PaperPosition');
    prePaperSize = get(gcf,'PaperSize');

    % Make changing paper type possible
    set(gcf,'PaperType','<custom>');

    % Set units to all be the same
    set(gcf,'PaperUnits','inches');
    set(gcf,'Units','inches');

    % Save the pdf
    print -dpdf Test.pdf;

    % Restore the previous settings
    set(gcf,'PaperType',prePaperType);
    set(gcf,'PaperUnits',prePaperUnits);
    set(gcf,'Units',preUnits);
    set(gcf,'PaperPosition',prePaperPosition);
    set(gcf,'PaperSize',prePaperSize);    
end

Multiple y axes in MATLAB (axis alignment issue when printing)

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