If you refer to the documentation on "Graphics Objects Hierarchy," you'll see that the plotting order is based on the sequence in which graphic objects are created. In your code, since the shaded area is plotted last, it should appear on top of the lines.
A solution to this should be using "uistack" function to bring the lines to the front. Apparently, If you go through the following MATLAB Answers post, people have noticed that using "uistack" does not seem to work with "yyaxis" and have adviced to use "SortMethod" property to fix this as a workaround.
Please check if the following workaround is effective for you:
clear; clc; close all;
Data = xlsread("FigureOfMeritResults.xlsx");
% Extract data
Date = Data(469:1908,1);
FoM = Data(469:1908,3);
GHI = Data(469:1908,4);
% Calculate the running average over 5 data points
FoM_avg = movmean(FoM, 5);
GHI_avg = movmean(GHI, 5);
dFoM = zeros(length(FoM),1) + mean(FoM);
ticks = {'12:00AM','4:00AM','8:00AM','12:00PM','4:00PM','8:00PM','12:00AM'};
fz = 15;
%%
fig = figure;
set(gcf,'Color','w','Units','inches')
set(gcf,'Position',[1,1,5,6])
GHI_color = [0.8 0.8 1];
yyaxis left;
p1 = scatter(Date, FoM, 'Marker', '.', 'SizeData', 15, 'MarkerFaceColor', "#0072BD");
hold on;
p2 = scatter(Date, dFoM, 'Marker', '_', 'SizeData', 15, 'MarkerFaceColor', 'black');
hold on;
ax = gca;
ax.YColor = 'k';
yyaxis right;
xData = [Date; flipud(Date)];
yData = [zeros(size(GHI)); flipud(GHI)];
fillHandle = fill(xData, yData, GHI_color,'EdgeColor','none');
hold on;
ax = gca;
ax.YColor = 'k';
xlabel('Time of Day (hrs)', 'FontSize', fz);
numTicks = length(ticks);
tickPositions = linspace(min(Date), max(Date), numTicks);
xticks(tickPositions);
xticklabels(ticks);
set(gca, 'FontSize', fz);
set(gca, 'SortMethod', 'depth')
ax = gca;
box on;
set(ax,'BoxStyle','full','LineWidth',2,'XGrid','off','XMinorTick','off','YGrid','off',...
'YMinorTick','on');
You can know more about 'SortMethod' by referring to the documentation below:
Hope this helps!
