examples.m

%% gramm examples
% Examples and how-tos for gramm
%% Example from the readme
% Here we plot the evolution of fuel economy of new cars bewteen 1970 and 1980 (carbig
% dataset). Gramm is used to easily separate groups on the basis of the number of
% cylinders of the cars (color), and on the basis of the region of origin of
% the cars (subplot columns). Both the raw data (points) and a glm fit with
% 95% confidence interval (line+shaded area) are plotted. 
%
% We stat by loading the sample data (structure created from the carbig
% dataset)
load example_data;
%%% 
% Create a gramm object, provide x (year of production) and y (fuel economy) data,
% color grouping data (number of cylinders) and select a subset of the data
g=gramm('x',cars.Model_Year,'y',cars.MPG,'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
%%% 
% Subdivide the data in subplots horizontally by region of origin using
% facet_grid()
g.facet_grid([],cars.Origin_Region);
%%%
% Plot raw data as points
g.geom_point();
%%%
% Plot linear fits of the data with associated confidence intervals
g.stat_glm();
%%%
% Set appropriate names for legends
g.set_names('column','Origin','x','Year of production','y','Fuel economy (MPG)','color','# Cylinders');
%%%
% Set figure title
g.set_title('Fuel economy of new cars between 1970 and 1982');
%%%
% Do the actual drawing
figure('Position',[100 100 800 400]);
g.draw();

%% Grouping options in gramm
% With gramm there are a lot ways to map groups to visual properties of
% plotted data, or even subplots.
% Providing grouping variables to change visual properties is done in the
% constructor call |gramm()|. Grouping variables that determine subplotting
% are provided by calls to the |facet_grid()| or |facet_wrap()| methods.
% Note that *all the mappings presented below can be combined*, i.e. it's
% possible to previde different variables to each of the options.
%
% In order to plot multiple, diferent gramm objects in the same figure, an array of gramm objects
% is created, and the |draw()| function called at the end on the whole array

clear g
g(1,1)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(1,1).geom_point();
g(1,1).set_names('x','Horsepower','y','MPG');
g(1,1).set_title('No groups');


g(1,2)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5,'color',cars.Cylinders);
g(1,2).geom_point();
g(1,2).set_names('x','Horsepower','y','MPG','color','# Cyl');
g(1,2).set_title('color');

g(1,3)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5,'lightness',cars.Cylinders);
g(1,3).geom_point();
g(1,3).set_names('x','Horsepower','y','MPG','lightness','# Cyl');
g(1,3).set_title('lightness');

g(2,1)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5,'size',cars.Cylinders);
g(2,1).geom_point();
g(2,1).set_names('x','Horsepower','y','MPG','size','# Cyl');
g(2,1).set_title('size');

g(2,2)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5,'marker',cars.Cylinders);
g(2,2).geom_point();
g(2,2).set_names('x','Horsepower','y','MPG','marker','# Cyl');
g(2,2).set_title('marker');

g(2,3)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5,'linestyle',cars.Cylinders);
g(2,3).geom_line();
g(2,3).set_names('x','Horsepower','y','MPG','linestyle','# Cyl');
g(2,3).set_title('linestyle');

g(3,1)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(3,1).facet_grid(cars.Cylinders,[]);
g(3,1).geom_point();
g(3,1).set_names('x','Horsepower','y','MPG','row','# Cyl');
g(3,1).set_title('subplot rows');


g(3,2)=gramm('x',cars.Horsepower,'y',cars.MPG,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(3,2).facet_grid([],cars.Cylinders);
g(3,2).geom_point();
g(3,2).set_names('x','Horsepower','y','MPG','column','# Cyl');
g(3,2).set_title('subplot columns');

figure('Position',[100 100 800 800]);
g.draw();

%% Methods for visualizing Y~X relationships with X as categorical variable
% The following methods can be used when Y data is continuous and X data discrete/categorical.
%
% Here we also use an array of gramm objects in order to have multiple gramm plots
% on the same figure. The gramm objects use the same data, so  we copy them after construction using the
% |copy()| method

clear g

g(1,1)=gramm('x',cars.Origin_Region,'y',cars.Horsepower,'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(1,2)=copy(g(1));
g(1,3)=copy(g(1));
g(2,1)=copy(g(1));
g(2,2)=copy(g(1));

%Raw data as scatter plot
g(1,1).geom_point();
g(1,1).set_title('geom_point()');

%Jittered scatter plot
g(1,2).geom_jitter('width',0.4,'height',0);
g(1,2).set_title('geom_jitter()');

%Averages with confidence interval
g(1,3).stat_summary('geom',{'bar','black_errorbar'});
g(1,3).set_title('stat_summary()');

%Boxplots
g(2,1).stat_boxplot();
g(2,1).set_title('stat_boxplot()');

%Violin plots
g(2,2).stat_violin('fill','transparent');
g(2,2).set_title('stat_violin()');

%These functions can be called on arrays of gramm objects
g.set_names('x','Origin','y','Horsepower','color','# Cyl');
g.set_title('Visualization of Y~X relationships with X as categorical variable');

figure('Position',[100 100 800 550]);
g.draw();


%% Methods for visualizing X densities
% The following methods can be used in order to represent the density of a continuous variable. Note that here
% we represent the same data as in the previous figure, this time with Horsepower as X
% (over which the densities are represented), and separating the region of
% origin with subplots.

clear g

g(1,1)=gramm('x',cars.Horsepower,'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(1,2)=copy(g(1));
g(2,1)=copy(g(1));
g(2,2)=copy(g(1));

%Raw data as raster plot
g(1,1).facet_grid(cars.Origin_Region,[]);
g(1,1).geom_raster();
g(1,1).set_title('geom_raster()');

%Histogram
g(1,2).facet_grid(cars.Origin_Region,[]);
g(1,2).stat_bin('nbins',8);
g(1,2).set_title('stat_bin()');

%Kernel smoothing density estimate
g(2,1).facet_grid(cars.Origin_Region,[]);
g(2,1).stat_density();
g(2,1).set_title('stat_density()');

% Q-Q plot for normality
g(2,2).facet_grid(cars.Origin_Region,[]);
g(2,2).stat_qq();
g(2,2).axe_property('XLim',[-5 5]);
g(2,2).set_title('stat_qq()');

g.set_names('x','Horsepower','color','# Cyl','row','','y','');
g.set_title('Visualization of X densities');
figure('Position',[100 100 800 550]);
g.draw();


%% Methods for visualizing Y~X relationship with both X and Y as continuous variables
% The following methods can be used when
% both X and Y data are continuous

clear g
%Raw data as scatter plot
g(1,1)=gramm('x',cars.Horsepower,'y',cars.Acceleration,'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(1,2)=copy(g(1));
g(1,3)=copy(g(1));
g(2,1)=copy(g(1));
g(2,2)=copy(g(1));

g(1,1).geom_point();
g(1,1).set_title('geom_point()');

%Generalized linear model fit
g(1,2).stat_glm();
g(1,2).set_title('stat_glm()');

%Custom fit with provided function
g(1,3).stat_fit('fun',@(a,b,c,x)a./(x+b)+c,'intopt','functional');
g(1,3).set_title('stat_fit(''fun'',@(a,b,c,x)a./(x+b)+c)');

%Spline smoothing
g(2,1).stat_smooth();
g(2,1).set_title('stat_smooth()');

%Moving average
g(2,2).stat_summary('bin_in',10);
g(2,2).set_title('stat_summary(''bin_in'',10)');

g.set_names('x','Horsepower','y','Acceleration','color','# Cylinders');

%Corner histogram
g(2,3)=gramm('x',(cars.Horsepower-nanmean(cars.Horsepower))/nanstd(cars.Horsepower),'y',-(cars.Acceleration-nanmean(cars.Acceleration))/nanstd(cars.Acceleration),'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(2,3).geom_point();
g(2,3).stat_cornerhist('edges',-4:0.2:4,'aspect',0.6)
g(2,3).geom_abline()
g(2,3).set_title('stat_cornerhist()');
g(2,3).set_names('x','z(Horsepower)','y','-z(Acceleration)')

g.set_title('Visualization of Y~X relationship with both X and Y as continuous variables');
figure('Position',[100 100 800 550]);
g.draw();


%% Methods for visualizing custom confidence intervals
% With |geom_interval()| it is possible to plot custom confidence intervals
% by provinding |'ymin'| and |'ymax'| values to |gramm()|. All options to
% display confidence intervals in |stat_summary()| are available, including
% dodging.

cars_table=struct2table(cars);
cars_summary=rowfun(@(hp)deal(nanmean(hp),bootci(200,@(x)nanmean(x),hp)'),cars_table(cars.Cylinders~=3 & cars.Cylinders~=5,:),...
    'InputVariables',{'Horsepower'},...
    'GroupingVariables',{'Origin_Region' 'Cylinders'},...
    'OutputVariableNames',{'hp_mean' 'hp_ci'});

clear g
%Bars and error bars
g(1,1)=gramm('x',cars_summary.Origin_Region,'y',cars_summary.hp_mean,...
    'ymin',cars_summary.hp_ci(:,1),'ymax',cars_summary.hp_ci(:,2),'color',cars_summary.Cylinders);
g(1,1).set_names('x','Origin','y','Horsepower','color','# Cylinders');
g(1,1).geom_bar('dodge',0.8,'width',0.6);
g(1,1).geom_interval('geom','black_errorbar','dodge',0.8,'width',1);

%points and error bars
g(1,2)=gramm('x',categorical(cars_summary.Cylinders),'y',cars_summary.hp_mean,...
    'ymin',cars_summary.hp_ci(:,1),'ymax',cars_summary.hp_ci(:,2),'color',cars_summary.Origin_Region);
g(1,2).set_names('color','Origin','y','Horsepower','x','# Cylinders');
g(1,3)=copy(g(1,2));
g(1,2).set_color_options('map','matlab');

g(1,2).geom_point('dodge',0.2);
g(1,2).geom_interval('geom','errorbar','dodge',0.2,'width',0.8);

%Shaded area
g(1,3).geom_interval('geom','area');

figure('Position',[100 100 800 450]);
g.axe_property('YLim',[-10 190]);
g.draw()


%% Methods for visualizing 2D densities
% The following methods can be used to visualize 2D densities for
% bivariate data

%Create point cloud with two categories
N=10^4;
x=randn(1,N);
y=x+randn(1,N);
test=repmat([0 1 0 0],1,N/4);
y(test==0)=y(test==0)+3;

clear g
% Display points and 95% percentile confidence ellipse
g(1,1)=gramm('x',x,'y',y,'color',test);
g(1,1).set_names('color','grp');
g(1,1).geom_point();
%'patch_opts' can be used to provide more options to the patch() internal
%call
g(1,1).stat_ellipse('type','95percentile','geom','area','patch_opts',{'FaceAlpha',0.1,'LineWidth',2});
g(1,1).set_title('stat_ellispe()');

%Plot point density as contour plot
g(1,2)=gramm('x',x,'y',y,'color',test);
g(1,2).stat_bin2d('nbins',[10 10],'geom','contour');
g(1,2).set_names('color','grp');
g(1,2).set_title('stat_bin2d(''geom'',''contour'')');

% %Plot density as point size (looks good only when axes have the same
% %scale, hence the 'DataAspectRatio' option, equivalent to axis equal)
% g(2,1)=gramm('x',x,'y',y,'color',test);
% g(2,1).stat_bin2d('nbins',{-10:0.4:10 ; -10:0.4:10},'geom','point');
% g(2,1).axe_property('DataAspectRatio',[1 1 1]);
% g(2,1).set_names('color','grp');
% g(2,1).set_title('stat_bin2d(''geom'',''point'')');

%Plot density as heatmaps (Heatmaps don't work with multiple colors, so we separate
%the categories with facets). With the heatmap we see better the
%distribution in high-density areas
g(2,1)=gramm('x',x,'y',y);
g(2,1).facet_grid([],test);
g(2,1).stat_bin2d('nbins',[20 20],'geom','image');
%g(2,1).set_continuous_color('LCH_colormap',[0 100 ; 100 20 ;30 20]); %Let's try a custom LCH colormap !
g(2,1).set_names('column','grp','color','count');
g(2,1).set_title('stat_bin2d(''geom'',''image'')');

g.set_title('Visualization of 2D densities');

figure('Position',[100 100 800 600])
g.draw();
%We change the point size in the first graph a posteriori
set([g(1,1).results.geom_point_handle],'MarkerSize',2);

%% Methods for visualizing repeated trajectories
% gramm supports 2D inputs for X and Y data (as 2D array or cell of
% arrays), which is particularly useful for representing repeated
% trajectories. Here for example we generate 50 trajectories, each of
% length 40. The grouping data is then given per trajectory and not per
% data point. Here the color grouping variable is thus given as a 1x50
% cellstr.

%We generate 50 trajectories of length 40, with 3 groups
N=50;
nx=40;
cval={'A' 'B' 'C'};
cind=randi(3,N,1);
c=cval(cind);
x=linspace(0,3,nx);
y=arrayfun(@(c)sin(x*c)+randn(1,nx)/10+x*randn/5,cind,'UniformOutput',false);

clear g
g(1,1)=gramm('x',x,'y',y,'color',c);
g(1,2)=copy(g(1));
g(2,1)=copy(g(1));
g(2,2)=copy(g(1));

g(1,1).geom_point();
g(1,1).set_title('geom_point()');

g(1,2).geom_line();
g(1,2).set_title('geom_line()');

g(2,1).stat_smooth();
g(2,1).set_title('stat_smooth()');


g(2,2).stat_summary();
g(2,2).set_title('stat_summary()');

g.set_title('Visualization of repeated trajectories ');

figure('Position',[100 100 800 550]);
g.draw();

%% Methods for visualizing repeated densities (e.g. spike densities)
% With the support of 2D inputs for X and gramm's functionality for
% representing the density of data, useful neuroscientific plots can be
% generated when the provided X corresponds to spike trains: raster plots
% and peristimulus time histograms (PSTHs).

%We generate 50 spike trains, with 3 groups
N=50;
cval={'A' 'B' 'C'};
cind=randi(3,N,1);
c=cval(cind);
train_template=[zeros(1,300)  ones(1,200)];
%Pseudo-poisson spike trains
spike_train=cell(N,1);
for k=1:N
    temp_train=rand*0.05+train_template/(cind(k)*8);
    U=rand(size(temp_train));
    spike_train{k}=find(U<temp_train);
end

clear g
g(1,1)=gramm('x',spike_train,'color',c);
g(1,1).geom_raster();
g(1,1).set_title('geom_raster()');

g(1,2)=gramm('x',spike_train,'color',c);
g(1,2).stat_bin('nbins',25,'geom','line');
g(1,2).set_title('stat_bin()');

g.set_names('x','Time','y','');
g.set_title('Visualization of spike densities');

figure('Position',[100 100 800 350]);
g.draw();

%% Options for separating groups across subplots with facet_grid()
% To separate groups in different rows and columns of sublots, the grouping
% variable just need to be passed to the
% |facet_grid(goup_rows,group_columns)| function or |facet_wrap(group_columns)|. Both have multiple
% options concerning the scaling of data between subplots.
%
% * By default |'scale','fixed'| all subplots have the same limits
% * |'scale','free_x'|: subplots on the same columns have the same x limits
% * |'scale','free_y'|: subplots on the same rows have the same y limits
% * |'scale','free'|: subplots on the same rows have the same y limits,
% subplots on the same columns have the same x limits
% * |'scale','independent'|: subplots have independent limits
%
% In |facet_grid()|; the |'space'| option allows to set how the subplot axes themselves scale with
% the data. It should be used in conjunction with the corresponding
% |'scale'| option.


% Generating fake data
N=2000;
colval={'A' 'B' 'C'};
rowval={'I' 'II'};
cind=randi(3,N,1);
c=colval(cind);
rind=randi(2,N,1);
r=rowval(rind);

x=randn(N,1);
y=randn(N,1);

x(cind==1 & rind==1)=x(cind==1  & rind==1)*5;
x=x+cind*3;
y(cind==3 & rind==2)=y(cind==3  & rind==2)*3;
y=y-rind*4;

clear g
g(1,1)=gramm('x',x,'y',y,'color',c,'lightness',r);
g(1,2)=copy(g(1));
g(2,1)=copy(g(1));
g(2,2)=copy(g(1));
g(3,1)=copy(g(1));
g(3,2)=copy(g(1));

g(1,1).geom_point();
g(1,1).set_title('No facets');

g(1,2).facet_grid(r,c);
g(1,2).geom_point();
g(1,2).no_legend();
g(1,2).set_title('facet_grid()');


g(2,1).facet_grid(r,c,'scale','free');
g(2,1).geom_point();
g(2,1).no_legend();
g(2,1).set_title('facet_grid(''scale'',''free'')');

g(2,2).facet_grid(r,c,'scale','free','space','free');
g(2,2).geom_point();
g(2,2).no_legend();
g(2,2).set_title('facet_grid(''scale'',''free'',''space'',''free'')');

g(3,1).facet_grid(r,c,'scale','free_x');
g(3,1).geom_point();
g(3,1).no_legend();
g(3,1).set_title('facet_grid(''scale'',''free_x'')');

g(3,2).facet_grid(r,c,'scale','independent');
g(3,2).geom_point();
g(3,2).no_legend();
g(3,2).set_title('facet_grid(''scale'',''independent'')');

g.set_color_options('lightness_range',[40 80],'chroma_range',[80 40]);
g.set_names('column','','row','');
%g.axe_property('color',[0.9 0.9 0.9],'XGrid','on','YGrid','on','GridColor',[1 1 1],'GridAlpha',0.8,'TickLength',[0 0],'XColor',[0.3 0.3 0.3],'YColor',[0.3 0.3 0.3])
g.set_title('facet_grid() options');

figure('Position',[100 100 800 800]);
g.draw();




%% Options for creating histograms with stat_bin() 
% Example of different |'geom'| options:
%
% * |'bar'| (default), where color groups are side-by-side (dodged)
% * |'stacked_bar'|
% * |'line'|
% * |'overlaid_bar'|
% * |'point'|
% * |'stairs'|


%Create variables
x=randn(1200,1)-1;
cat=repmat([1 1 1 2],300,1);
x(cat==2)=x(cat==2)+2;

clear g5
g5(1,1)=gramm('x',x,'color',cat);
g5(1,2)=copy(g5(1));
g5(1,3)=copy(g5(1));
g5(2,1)=copy(g5(1));
g5(2,2)=copy(g5(1));
g5(2,3)=copy(g5(1));

g5(1,1).stat_bin(); %by default, 'geom' is 'bar', where color groups are side-by-side (dodged)
g5(1,1).set_title('''bar'' (default)');

g5(1,2).stat_bin('geom','stacked_bar'); %Stacked bars option
g5(1,2).set_title('''stacked_bar''');

g5(2,1).stat_bin('geom','line'); %Draw lines instead of bars, easier to visualize when lots of categories, default fill to edges !
g5(2,1).set_title('''line''');

g5(2,2).stat_bin('geom','overlaid_bar'); %Overlaid bar automatically changes bar coloring to transparent
g5(2,2).set_title('''overlaid_bar''');

g5(1,3).stat_bin('geom','point'); 
g5(1,3).set_title('''point''');


g5(2,3).stat_bin('geom','stairs'); %Default fill is edges
g5(2,3).set_title('''stairs''');

g5.set_title('''geom'' options for stat_bin()');

figure('Position',[100 100 800 600]);
g5.draw();

%%
% Example of alternative |'fill'| options
%
% * |'face'|
% * |'all'|
% * |'edge'|
% * |'transparent'|

clear g6
g6(1,1)=gramm('x',x,'color',cat);
g6(1,2)=copy(g6(1));
g6(1,3)=copy(g6(1));
g6(2,1)=copy(g6(1));
g6(2,2)=copy(g6(1));
g6(2,3)=copy(g6(1));


g6(1,1).stat_bin('fill','face');
g6(1,1).set_title('''face''');

g6(1,2).stat_bin('fill','transparent');
g6(1,2).set_title('''transparent''');

g6(1,3).stat_bin('fill','all');
g6(1,3).set_title('''all''');

g6(2,1).stat_bin('fill','edge');
g6(2,1).set_title('''edge''');

g6(2,2).stat_bin('geom','stairs','fill','transparent');
g6(2,2).set_title('''transparent''');


g6(2,3).stat_bin('geom','line','fill','all');
g6(2,3).set_title('''all''');

g6.set_title('''fill'' options for stat_bin()');

figure('Position',[100 100 800 600]);
g6.draw();

%%
% Examples of other histogram-generation options
%
% * Default binning
% * |'normalization','probability'|
% * |'normalization','cumcount'|
% * |'normalization','cdf'|
% * |'edges',-1:0.5:10|
% * |'normalization','countdensity'| and custom edges

clear g7
g7(1,1)=gramm('x',x,'color',cat);
g7(1,2)=copy(g7(1));
g7(1,3)=copy(g7(1));
g7(2,1)=copy(g7(1));
g7(2,2)=copy(g7(1));
g7(2,3)=copy(g7(1));

g7(1,1).stat_bin('geom','overlaid_bar'); %Default binning (30 bins)

%Normalization to 'probability'
g7(2,1).stat_bin('normalization','probability','geom','overlaid_bar');
g7(2,1).set_title('''normalization'',''probability''','FontSize',10);

%Normalization to cumulative count
g7(1,2).stat_bin('normalization','cumcount','geom','stairs');
g7(1,2).set_title('''normalization'',''cumcount''','FontSize',10);

%Normalization to cumulative density
g7(2,2).stat_bin('normalization','cdf','geom','stairs');
g7(2,2).set_title('''normalization'',''cdf''','FontSize',10);

%Custom edges for the bins
g7(1,3).stat_bin('edges',-1:0.5:10,'geom','overlaid_bar');
g7(1,3).set_title('''edges'',-1:0.5:10','FontSize',10);

%Custom edges with non-constand width (normalization 'countdensity'
%recommended)
g7(2,3).stat_bin('geom','overlaid_bar','normalization','countdensity','edges',[-5 -4 -2 -1 -0.5 -0.25 0 0.25 0.5  1 2 4 5]);
g7(2,3).set_title({'''normalization'',''countdensity'',' '''edges'',' '[-5 -4 -2 -1 -0.5 -0.25 0 0.25 0.5  1 2 4 5]'},'FontSize',10);

g7.set_title('Other options for stat_bin()');

figure('Position',[100 100 800 600]);
g7.draw();

%% Visualize x-y difference with inset histogram using stat_cornerhist()


%Generate sample data
N=200;
x=randn(1,N*4);
y=x+randn(1,N*4)/2;
c=repmat([1 2],1,N*2);
b=repmat([1 2 2 2],1,N);
y(c==1 & b==2)=y(c==1 & b==2)+2;


clear g
g=gramm('x',x,'y',y,'color',c);
g.facet_grid([],b);
g.geom_point();
g.stat_cornerhist('edges',-4:0.1:2,'aspect',0.5);
g.geom_abline();

g.set_title('Visualize x-y with stat_cornerhist()');
figure('Position',[100 100 800 600]);
g.draw();

%Possibility to use axe handles of the inset axes to add elements or change
%properties
plot(g.results.stat_cornerhist(2).child_axe_handle,[-2 -2],[0 50],'k:','LineWidth',2)
%set([g.results.stat_cornerhist.child_axe_handle],'XTick',[])


%% Graphic and normalization options in stat_violin()

clear g
g(1,1)=gramm('x',cars.Origin_Region,'y',cars.Horsepower,'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(1,1).set_names('x','Origin','y','Horsepower','color','# Cyl');
g(1,2)=copy(g(1,1));
g(1,3)=copy(g(1,1));
g(2,1)=copy(g(1,1));
g(2,2)=copy(g(1,1));

%Jittered scatter plot
g(1,1).geom_jitter('width',0.6,'height',0,'dodge',0.7);
g(1,1).set_title('jittered data');


g(1,2).stat_violin('normalization','area');
g(1,2).set_title('''normalization'',''area'' (Default)');

g(1,3).stat_violin('normalization','width');
g(1,3).set_title('''normalization'',''width''');

g(2,1).stat_violin('normalization','count','fill','all');
g(2,1).set_title('''normalization'',''count'' , ''fill'',''all''');

g(2,2).stat_violin('half',true,'normalization','count','width',1,'fill','transparent');
g(2,2).set_title('''half'',true , ''fill'',''transparent''');

g(2,3)=gramm('x',cars.Origin_Region,'y',cars.Horsepower,'color',cars.Origin_Region,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g(2,3).set_names('x','Origin','y','Horsepower','color','Origin');
g(2,3).stat_violin('normalization','area','dodge',0,'fill','edge');
g(2,3).stat_boxplot('width',0.15);
g(2,3).set_title('with stat_boxplot()');
g(2,3).set_color_options('map','brewer_dark');

g.set_title('Options for stat_violin()');
figure('Position',[100 100 800 600]);
g.draw();



%% Options for dodging and spacing graphic elements in |stat_summary()| and |stat_boxplot()|
% |stat_summary()| and |stat_boxplot()|, as well as |stat_bin()|, use a pair of options for
% setting the width of graphical elements (|'width'|) and setting how
% elements of different colors can be dodged to the side to avoid overlap
% (|'dodge'|)

%Create data
x=repmat(1:10,1,100);
catx=repmat({'A' 'B' 'C' 'F' 'E' 'D' 'G' 'H' 'I' 'J'},1,100);
y=randn(1,1000)*3;
c=repmat([1 1 1 1 1 1 1 1 1 1    1 1 2 2 2 2 2 3 2 2     2 1 1 2 2 2 2 3 2 3     2 1 1 2 2 2 2 2 2 2],1,25);
y=2+y+x+c*0.5;


clear g
g(1,1)=gramm('x',catx,'y',y,'color',c);
g(2,1)=copy(g(1));
g(3,1)=copy(g(1));
g(4,1)=copy(g(1));
g(5,1)=copy(g(1));


g(1,1).stat_boxplot();
g(1,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');
g(1,1).set_title('''width'',0.6,''dodge'',0.7 (Default)');

g(2,1).stat_boxplot('width',0.5,'dodge',0);
g(2,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');
g(2,1).set_title('''width'',0.5,''dodge'',0');

g(3,1).stat_boxplot('width',1,'dodge',1);
g(3,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');
g(3,1).set_title('''width'',1,''dodge'',1');

g(4,1).stat_boxplot('width',0.6,'dodge',0.4);
g(4,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');
g(4,1).set_title('''width'',0.6,''dodge'',0.4');

g(5,1).facet_grid([],c);
g(5,1).stat_boxplot('width',0.5,'dodge',0,'notch',true);
g(5,1).set_title('''width'',0.5,''dodge'',0,''notch'',true');

g.set_title('Dodge and spacing options for stat_boxplot()');

figure('Position',[100 100 800 1000]);
g.draw();

%%
% With |stat_summary()|, |'width'| controls the width of bars and error bars.



clear g
g(1,1)=gramm('x',catx,'y',y,'color',c);
g(2,1)=copy(g(1));
g(3,1)=copy(g(1));
g(4,1)=copy(g(1));
g(5,1)=copy(g(1));

g(1,1).stat_summary('geom',{'bar' 'black_errorbar'},'setylim',true);
g(1,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');
g(1,1).set_title('Default dodging with ''geom'',''bar''');

g(2,1).stat_summary('geom',{'bar' 'black_errorbar'},'dodge',0.7,'width',0.7);
g(2,1).set_title('''dodge'',0.7,''width'',0.7');
g(2,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');

g(3,1).stat_summary('geom',{'area'});
g(3,1).set_title('''geom'',''area''');
g(3,1).set_title('No dodging with ''geom'',''area''');

g(4,1).stat_summary('geom',{'point' 'errorbar'},'dodge',0.3,'width',0.5);
g(4,1).set_title('''dodge'',0.3,''width'',0.5');
g(4,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');

g(5,1).facet_grid([],c);
g(5,1).stat_summary('geom',{'bar' 'black_errorbar'},'width',0.5,'dodge',0);
g(5,1).set_title('''width'',0.5,''dodge'',0');

g.set_title('Dodge and width options for stat_summary()');

figure('Position',[100 100 800 1000]);
g.draw();

%% Using different groups for different stat_ and geom_ methods by superimposing gramm plots
% By using the method update() after a first draw() call of a gramm object,
% it is possible to add or remove grouping variables.
% Here in a first gramm plot we make a glm fit of cars Acceleration as a
% function of Horsepower, across all countries and number of cylinders, and
% change the color options so that the fit appears in grey

clear g10
figure('Position',[100 100 600 450]);
g10=gramm('x',cars.Horsepower,'y',cars.Acceleration,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g10.set_names('color','# Cylinders','x','Horsepower','y','Acceleration','Column','Origin');
g10.set_color_options('chroma',0,'lightness',30);
g10.stat_glm('geom','area','disp_fit',false);
g10.draw()
snapnow;

%%
% After the first draw() call (optional), we call the update() method by specifying a
% new grouping variable determining colors. We also change the facet_grid()
% options, which will duplicate the fit made earlier across all new facets.
% Last, color options are reinitialized to default values

g10.update('color',cars.Cylinders);
g10.facet_grid([],cars.Origin_Region);
g10.set_color_options();
g10.geom_point();
g10.draw();


%% Customizing color maps with set_color_options()
% With the method set_color_options(), automatic color generation for
% color and lightness groups can be tweaked

%Default: LCH-based colormap with hue variation
clear g
g(1,1)=gramm('x',cars.Origin,'y',cars.Horsepower,'color',cars.Origin);
g(1,2)=copy(g(1));
g(1,3)=gramm('x',cars.Origin,'y',cars.Horsepower,'lightness',cars.Origin);
g(2,1)=copy(g(1));
g(2,2)=copy(g(1));
g(2,3)=copy(g(1));


g(1,1).stat_summary('geom',{'bar'},'dodge',0);
g(1,1).set_title('Default LCH (''color'' groups)','FontSize',12);

%Possibility to change the hue range as well as lightness and chroma of
%the LCH-based colormap
g(1,2).stat_summary('geom',{'bar'},'dodge',0);
g(1,2).set_color_options('hue_range',[-60 60],'chroma',40,'lightness',90);
g(1,2).set_title('Modified LCH (''color'' groups)','FontSize',12);

%Possibility to change the lightness and chroma range of the LCH-based
%colormap when a 'lightness' variable is given
g(1,3).stat_summary('geom',{'bar'},'dodge',0);
g(1,3).set_color_options('lightness_range',[0 95],'chroma_range',[0 0]);
g(1,3).set_title('Modified LCH (''lightness'' groups)','FontSize',12);

%Go back to Matlab's defauls colormap
g(2,1).stat_summary('geom',{'bar'},'dodge',0);
g(2,1).set_color_options('map','matlab');
g(2,1).set_title('Matlab 2014B+ ','FontSize',12);

%Brewer colormap 1
g(2,2).stat_summary('geom',{'bar'},'dodge',0);
g(2,2).set_color_options('map','brewer1');
g(2,2).set_title('Color Brewer 1','FontSize',12);

%Brewer colormap 2
g(2,3).stat_summary('geom',{'bar'},'dodge',0);
g(2,3).set_color_options('map','brewer2');
g(2,3).set_title('Color Brewer 2','FontSize',12);

%Some methods can be called on all objects at the same time !
g.axe_property('YLim',[0 140]);
g.axe_property('XTickLabelRotation',60); %Should work for recent Matlab versions
g.set_names('x','Origin','y','Horsepower','color','Origin','lightness','Origin');
g.set_title('Colormap customizations examples');

figure('Position',[100 100 800 600])
g.draw();

%% Using a continuous color scale
% When the variable provided as 'color' contains too many different values
% (>15), or when set_continuous_color is used, gramm switches from a
% categorical color scale to a gradient-based continuous color scale.

load spectra.mat

%Here we create x as a 1xN array (see example above), and use a MxN matrix
%for y. Color applies to the M rows of y.
g18=gramm('x',900:2:1700,'y',NIR,'color',octane);
g18.set_names('x','Wavelength (nm)','y','NIR','color','Octane');
g18.set_continuous_color('colormap','hot');
g18.geom_line;
figure('Position',[100 100 800 450]);
g18.draw();

%% Changing the order of elements with set_order_options()
% By default, gramm uses grouping data in increasing order of the group
% value (alphabetical for cellstr, numerical for arrays). Using
% set_order_options(), it is possible to fine tweak the orders of color,
% lightness, facet rows and columns, as well as categorical X

y=[36 38 40 42 44 46];
x={'XS' 'S' 'M' 'L' 'XL' 'XXL'};


clear g
%By default, both x and lightness are ordered according to sorted (here
%alphabetically) input
g(1,2)=gramm('x',x,'y',y,'lightness',x);
g(1,2).stat_summary('geom','bar','dodge',0);
g(1,2).set_title('Default output');


%By using set_order_options('x',0), x are presented in the raw input order. The
%color is still sorted
g(2,1)=gramm('x',x,'y',y,'lightness',x);
g(2,1).stat_summary('geom','bar','dodge',0);
g(2,1).set_order_options('x',0);
g(2,1).set_title('x in input order');

%By using set_order_options('x',0,'lightness',{'XS' 'S' 'M' 'L' 'XL'
%'XXL'}), we also order lightness in the desired order, here by
%directly providing the desired order.
g(2,2)=gramm('x',x,'y',y,'lightness',x);
g(2,2).stat_summary('geom','bar','dodge',0);
g(2,2).set_order_options('x',0,'lightness',{'XS' 'S' 'M' 'L' 'XL' 'XXL'});
g(2,2).set_title({'x in input order' 'lightness in custom order'});
%Examples below properly fail
%g(2,2).set_order_options('x',0,'lightness',{'XXL' 'XL' 'L' 'M' 'S' 'B'})
%g(2,2).set_order_options('x',0,'lightness',{'XXL' 'XL' 'L' 'M' 'S' 1})
%g(2,2).set_order_options('x',0,'lightness',{'XXL' 'XL' 'L' 'M' 'S'})

%It is also possible to set up a custom order (indices within the sorted
%input), here used to inverse lightness map. This way is a bit more
%practical for floating point numerical variables. For cells of string, the
%way above is easier.
g(2,3)=gramm('x',x,'y',y,'lightness',x);
g(2,3).stat_summary('geom','bar','dodge',0);
g(2,3).set_order_options('x',0,'lightness',[6 4 1 2 3 5]);
g(2,3).set_title({'x in input order' 'lightness in custom order'});
%Exampel below properly fail
%g(2,3).set_order_options('x',0,'lightness',[6 4 1 2 3 3])

g.set_names('x','US size','y','EU size','lightness','US size');
g.axe_property('YLim',[0 48]);

figure('Position',[100 100 800 600]);
g.draw();

%% Advanced customization of gramm figures
% The options for the geom_ and stat_ methods, as well as the
% |axe_property()| method allow for high-level customization of gramm figures. Since
% the gramm object allows access to all handles for graphical objects, it's
% also possible to do more precise customizations and modifications of a
% gramm figure once it's drawn. In this figure:
%
% * Y grid is turned on on all facets with |axe_property('YGrid','on')|
% * A vertical line and text is added to only one of the facets by using
% the |facet_axes_handles| public property of gramm objects
% * All points are made smaller by using their handles 
% |results.grom_point_handle| in the |set()| function
% * Similarly, all confidence areas are made grey |g.results.stat_glm.area_handle|
% * A subset of the glm lines are made thicker by calling |set()| on a
% subset teir handles |g.results.stat_glm(g.results.color==4).line_handle]
% 
% It is also possible to set where the gramm
% axes are drawn by using the |set_parent(parent_handle)| function, which receives the
% handle of a figure/uipanel/uitab object to use as parent as argument.

f=figure('Position',[100 100 800 500]);
%Create fake button
c=uicontrol('Style','pushbutton','String','Dummy','Units','normalized','Position',[0.8 0.45 0.15 0.1]);
%Create uipanel to put our gramm plots
p=uipanel('Position',[0.05 0.1 0.7 0.8],'Parent',f,'BackgroundColor',[1 1 1]);

% Starting with the example figure
load example_data;
g=gramm('x',cars.Model_Year,'y',cars.MPG,'color',cars.Cylinders,'subset',cars.Cylinders~=3 & cars.Cylinders~=5);
g.facet_grid([],cars.Origin_Region);
g.stat_glm();
g.geom_point();
g.set_names('column','Origin','x','Year of production','y','Fuel economy (MPG)','color','# Cylinders');
g.set_title('Fuel economy of new cars between 1970 and 1982');
g.axe_property('YGrid','on');
g.set_parent(p);
g.draw();

%It's possible to use the axes handles to add elements to single axes
line([75 75],[0 50],'Color','k','LineStyle','--','Parent',g.facet_axes_handles(1));
text(75.3,47,'Important event','Parent',g.facet_axes_handles(1));

%It's also possible to change properties of graphical elements
%Either all at once
set([g.results.geom_point_handle],'MarkerSize',5);
set([g.results.stat_glm.area_handle],'FaceColor',[0.4 0.4 0.4]);
%Or on a subset of them (here only for the lines of glms of 4-cylinder cars)
set([g.results.stat_glm(g.results.color==4).line_handle],'LineWidth',3);


%% Using different input formats for x and y (1D arrays, cells of arrays, 2D arrays)
% Standard ggplot-like input (arrays for everything)
% Note the continuous line connecting all blue data points, gramm can't know
% when to start a new line in this case
Y=[1 2 3 4 5 2 3 4 5 6 3 4 5 6 7];
X=[1 2 3 4 5 0 1 2 3 4 -1 0 1 2 3];
C=[1 1 1 1 1 2 2 2 2 2 2 2 2 2 2];
figure
g11=gramm('x',X,'y',Y,'color',C);
g11.geom_line();
g11.draw();

%%
% Adding a group variable solves the problem in a ggplot-like way
G=[1 1 1 1 1 2 2 2 2 2 3 3 3 3 3];
figure
g12=gramm('x',X,'y',Y,'color',C,'group',G);
g12.geom_line();
g12.draw();

%%
% For a more matlab-like solution, Y and X can be 2D arrays, rows will automatically be considered as groups.
% as a consequence grouping data (color, etc...) are provided for the rows !
Y=[1 2 3 4 5;2 3 4 5 6; 3 4 5 6 7];
X=[1 2 3 4 5; 0 1 2 3 4; -1 0 1 2 3];
C=[1 2 2];
figure
g13=gramm('x',X,'y',Y,'color',C);
g13.geom_line();
g13.draw();

%%
% If all X values are the same, it's possible to provide X as a single row
X=[1 2 3 4 5];
figure
g14=gramm('x',X,'y',Y,'color',C);
g14.geom_line();
g14.draw();

%%
% Similar results can be obtained with cells of arrays
Y={[1 2 3 4 5] [2 3 4 5 6] [3 4 5 6 7]};
X={[1 2 3 4 5] [0 1 2 3 4] [-1 0 1 2 3]};
figure
g15=gramm('x',X,'y',Y,'color',C);
g15.geom_line();
g15.draw();

Y={[1 2 3 4 5] [2 3 4 5 6] [3 4 5 6 7]};
X=[1 2 3 4 5];
figure
g16=gramm('x',X,'y',Y,'color',C);
g16.geom_line();
g16.draw();

%%
% With cells of arrays, there is the opportunity to have different lengths
% for different groups
Y={[1 2 3 4 5] [3 4 5] [3 4 5 6 7]};
X={[1 2 3 4 5] [1 2 3] [-1 0 1 2 3]};
figure
g17=gramm('x',X,'y',Y,'color',C);
g17.geom_line();
g17.draw();