Matlab does not allow to combine use more than one colormap in a figure. However there are some possibilities to get around this problem, which are presented in this article.

Initialization and export of figure

For all plots the same initialization for the data and the figure is used:

% clear command window, figures and all variables
clc; clf; clear all; 
 
%% Common variables
 
FontSize = 12;
FontName = 'MyriadPro-Regular'; % or choose any other font
 
doExportPlot = true;
 
%% Plot variables
SaveDir = '';
 
TITLE = '';
    xLabelText = 'x-values';
    yLabelText = 'y-values';
    zLabelText = 'function values';
 
 
%%
SaveDir = '';
BaseDir = '';
%% Create Data
[x y data] = peaks(1000);
data = data - min(min(<span class="hiddenGrammarError" pre="">data));
data</span> = data / max(max(data));
 
%% start plot
 
% figure dimensions in cm. I choose 1.5 or 2 times 
% the target size typically. If figure is display in
% document much smaller increase the fontsize.
 
figure_width = 14;  
figure_height = 10;
 
% --- setup plot windows
figuresVisible = 'on'; % 'off' for non displayed plots (will still be exported)
hfig = figure(1); clf;
    set(hfig,'Visible', figuresVisible)
 
    set(hfig, 'units', 'centimeters', 'pos', [5 5 figure_width figure_height])   
    set(hfig, 'PaperPositionMode', 'auto');    
    set(hfig, 'Renderer','zbuffer'); 
    set(hfig, 'Color', [1 1 1]); % Sets figure background
    set(gca, 'Color', [1 1 1]); % Sets axes background
 
% --- dimensions and position of plot 
hsp = subplot(1,1,1, 'Parent', hfig);
set(hsp,'Position',[0.12 0.15 0.80 0.8]);
 
colorDepth = 1000;

And the same code is used to style the plot and export the figure:

%%  setup axis plot properties
% shading interp; % interpolate pixels
axis on;      % display axis
axis tight;   % no white borders
 
set(gca, ...
    'Box'         , 'on'      , ...
    'TickDir'     , 'in'      , ...
    'TickLength'  , [.02 .02] , ...
    'XMinorTick'  , 'off'      , ...
    'YMinorTick'  , 'off'     , ...
    'XGrid'       , 'off'     , ...
    'YGrid'       , 'off'     , ...
    'XColor'      , [.0 .0 .0], ...
    'YColor'      , [.0 .0 .0], ...
    'LineWidth'   , 0.6        );
 
%% axis scales
 
% set(gca,'XTick',-15:5:15)
% set(gca,'YTick',-10:5:10)
 
%% label texts
 
% save handles to set up label properties
hTitle = title(TITLE);
hXLabel = xlabel(xLabelText);
hYLabel = ylabel(yLabelText);
 
%% set properties for all handles
set([gca, hTitle, hXLabel, hYLabel], ...
    'FontSize'   , FontSize    , ...
    'FontName'   , FontName);
 
 
%% last 'bug' fixes
 
% bring axis on top again (fix matlab bug)
set(gca,'Layer', 'top');
 
%% export
drawnow
 
doExportPlot = true;
if (doExportPlot)
    IMAGENAME = [SaveDir SaveName]; 
    print(hfig, ['-r' num2str(400)], [IMAGENAME '.png' ], ['-d' 'png']);    
end