My eventual solution (temperatures is the same as parameter_one, res_times is parameter_two, while full_FWHM is results):
% The unique temperatures are found and sorted after size
b = unique(temperatures);
% Finds the number of different temperatures used
c = size(b,1);
map = colormap(jet(c)); % Creates c different colours on the jet scale
i = 1; % Running integer needed in the if-loop
k = 1; % Running integer needed in the while-loop
% Loop then plots the points
while k < size(res_times,1)+1
% First, we figure out which temperature index the point to be plotted
% corresponds to
eval_temp = temperatures(k);
if eval_temp == b(i)
% If the temperature is equal to the i'th unique value in the
% temperature array, the point is plotted using the i'th color in
% the colorlist map
p = plot(res_times(k),full_FWHM(k),'o','MarkerFaceColor',...
map(i,:),'MarkerSize',6,'MarkerEdgeColor','k');
% The next few lines are merely to make sure the point is removed from the
% legend
hAnnotation = get(p,'Annotation');
hLegendEntry = get(hAnnotation,'LegendInformation');
set(hLegendEntry,'IconDisplayStyle','off')
% Since we have found a match, we need to reset the index and
% increase the loop value by one
i = 1;
k = k+1;
else
% If the temperature evaluated is not equal to the i'th unique
% temperature, the index i is increased by one, and we try again
i = i+1;
end
end
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