I gather that you want to have the boxes filled as in Alternative 1 and the x-ticks and labels as in Alternative 2.
See if using the option 'BoxStyle','filled' in boxplotGroup is sufficient:
% Unique value of 2 variables
Var1unique = ["Type 1", "Type 2", "Type 3"];
Var2unique = ["Group A", "Group B", "Group C", "Group D", "Group E"];
% Create the variable value of the same length to put in the table
Var1single = categorical(repelem(Var1unique.', 5));
Var2single = categorical(repmat(Var2unique.', 3, 1));
Var1 = repmat(Var1single,10,1);
Var2 = repmat(Var2single,10,1);
Yvalue = rand(150,1);
data = table( Var1, Var2, Yvalue);
LegendLabels = [ ...
"(A) Option A", ...
"(B) Option B", ...
"(C) Option C", ...
"(D) Option D", ...
"(E) Option E", ...
];
AxisLabels = {"A", "B", "C", "D", "E"};
%% Alternative 2
colorGroup = [ ...
0 0.4470 0.7410; ...
0.8500 0.3250 0.0980; ...
0.9290 0.6940 0.1250; ...
0.4940 0.1840 0.5560; ...
0.4660 0.6740 0.1880; ...
];
colors = repmat(colorGroup, 3, 1);
% Reshape data
datacell = cell(1, numel(Var2unique));
for var2Idx = 1:numel(Var2unique)
Idx1 = (data.Var1 == Var1unique(1) & data.Var2 == Var2unique(var2Idx));
Idx2 = (data.Var1 == Var1unique(1) & data.Var2 == Var2unique(var2Idx));
Idx3 = (data.Var1 == Var1unique(3) & data.Var2 == Var2unique(var2Idx));
datacell{1,var2Idx} = [table2array(data(Idx1, 3)), table2array(data(Idx2, 3)), table2array(data(Idx3, 3))];
end
plot2 = figure;
boxplotGroup(datacell,'groupLines', true , 'interGroupSpace',2, ...
'primaryLabels', AxisLabels, ...
'secondaryLabels',{'Type 1', 'Type 2', 'Type 3'}, ...
'Colors', colorGroup, ...
'Symbol', "o", 'BoxStyle','filled');
set(gca,'LineWidth',2, ...
'YGrid','on', ...
'GridLineWidth', 1);
set(findobj(gcf,'type','axes'),'FontName','Helvetica','FontSize',10, ...
'FontWeight','Bold','LineWidth', 1.5);
