missing parts of a figure when converting to pdf

When I use exportgraphics (or print) to convert a matlab .fig file to a .pdf file, the markers near the yaxes missing.

The .fig looks like this

And the .pdf produced looks like this

The following are the code producing the .fig

f1 = figure;
f1.Position = [400, 300, 650, 450];

yyaxis left

f1_p1 = plot(ana_nl_rng, ana_w1_dl_vec, "--", "LineWidth", 1.1, "Color", "#0072BD");
hold on
f1_p2 = plot(sim_nl_rng, sim_w1_dl_vec, "x", "MarkerSize", 7.0, "LineWidth", 0.8, "Color", "#0072BD");

f1_p3 = plot(ana_ns_rng, ana_w1_ds_vec, "-.", "LineWidth", 1.1, "Color", "#D95319");
f1_p4 = plot(sim_ns_rng, sim_w1_ds_vec, "o", "MarkerSize", 7.0, "LineWidth", 0.8, "Color", "#D95319");

ylim([0, 30]);
set(gca,'YColor','k');
ylabel("$D^{(\phi)}$", "Interpreter", "latex", "FontSize", 14, "Rotation", 0, ...
    'Units', 'normalized', 'Position', [-0.08, 0.53, 0.5]);

yyaxis right

f1_p5 = plot(ana_nl_rng, ana_nl_rng .* ana_w1_dl_vec + ana_ns_rng .* ana_w1_ds_vec, "-", "LineWidth", 1.1, ...
    "Color", "#EDB120");
f1_p6 = plot(sim_nl_rng, sim_nl_rng .* sim_w1_dl_vec + sim_ns_rng .* sim_w1_ds_vec, "+", "MarkerSize", 7.0, ... 
    "LineWidth", 0.8, "Color", "#EDB120");

set(gca,'YColor','k');
ylabel("$\hat{D}$", "Interpreter", "latex", "FontSize", 14, "Rotation", 0, ...
    'Units', 'normalized', 'Position', [1.09, 0.6, 0.5]);
ylim([120, 200]);
yticks(120:20:200);

xlim([5, 100]);
xticks([5, 10:10:100]);
xlabel("$n^{(LB)}$", "Interpreter", "latex", "FontSize", 15);
set(gca,'XTickLabel', get(gca,'XTickLabel'), 'FontSize', 14);

f1_ax1 = axes("Position", get(gca,"Position"), "Visible", 'off');
legend(f1_ax1, [f1_p1, f1_p2], ["Analysis", "Simulation"], "FontSize", 12);

f1_ax2 = axes("Position", get(gca,"Position"), "Visible", "off");
legend(f1_ax2, [f1_p3, f1_p4], ["Analysis", "Simulation"], "FontSize", 12);

f1_ax3 = axes("Position", get(gca,"Position"), "Visible","off");
legend(f1_ax3, [f1_p5, f1_p6], ["Analysis", "Simulation"], "FontSize", 12);

I added some arrows and textboxes manually afterwards, and I used the exportgraphics function to produce the .pdf

exportgraphics(f1, "./pdfs/dr_vs_n_fix_w_1.pdf")

Can anyone help me figure out what's the problem? Thank you!

[Jan]

What happens, if you create the axes with an disabled clipping?

axes('Clipping', 'off')

@Jie Zhang: Please use flags to inform admins and editors about inappropriate contributions, e.g. rudeness or off-topic messages. Thanks! I've posted this comment as an answer also, such that it can be marked as a solution.

[Walter Roberson]

You could experiment with https://www.mathworks.com/help/matlab/ref/matlab.graphics.axis.axes-properties.html#budumk7_sep_shared-Layer setting the axes 'Layer' property to 'bottom' . It should be 'bottom' by default, but it just might make a difference, maybe.

You could also use xlim and ylim to make the axes slightly bigger so that the end points are inside the drawing area.

Answer 1

[Jan]

Copied from my suggestion in the comments:

Disable the clipping of the axes object:

axes('Clipping', 'off')