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Harmonization of 'width' and 'dodge' arguments. Enhancements in stat_…
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…summary()

- stat_summary(), stat_bin(), and stat_boxplot() have coherent ‘width’
and ‘dodge’ arguments
- stat_summary() behaves better when data is missing or NaN
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@piermorel
piermorel committed Apr 14, 2016
1 parent 5bebb47 commit 2a0db69
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -80,6 +80,7 @@ Type <code>doc gramm</code> to find links to the documentation of each method.
- Possibility to customize color generations in the LCH color space, chose alternative colormaps (Matlab's default, [colorbrewer2](http://colorbrewer2.org)), or provide a custom colormap (<code>set_color_options()</code>)
- Possibility to change ordering of grouping variables between native, sorted, or custom (<code>set_order_options</code>)
- Confidence intervals as shaded areas, error bars or thin lines
- Set the width and dodging of graphical elements in <code>stat_bin()</code>, <code>stat_summary()</code>, and <code>stat_boxplot()</code>, with <code>'width'</code> and <code>'dodge'</code> arguments
- Results of computations from <code>stat_</code> plots are returned in the member structure <code>results</code>
- Figure title (<code>set_title()</code>)
- Multiple gramm plots can be combined in the same figure by creating a matrix of gramm objects and calling the <code>draw()</code> method on the whole matrix. An overarching title can be added by calling <code>set_title()</code> on the whole matrix.
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178 changes: 126 additions & 52 deletions examples.m
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@@ -1,3 +1,5 @@
saveimg=false;

%% Generate fake data

N=400
Expand Down Expand Up @@ -46,7 +48,7 @@
g2(1,1)=gramm('x',x,'y',y,'color',fouraltc);
g2(1,1).facet_grid(twoaltc,twoaltcb); %,'scales','independent'
g2(1,1).stat_smooth('lambda',1000,'geom','area');
g2(1,1).geom_point();
%g2(1,1).geom_point();

%Also works with categorical data
g2(1,2)=gramm('x',y,'y',x,'color',categorical(twoaltc));
Expand All @@ -63,9 +65,12 @@
g2(2,2).set_limit_extra(0.1,0);

%And call the draw function on the whole array !
figure
figure('Position',[100 100 800 600])
g2.draw();

if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/multiple_gramm_example','-dpng','-r0')
end


%% Scaling options for faceting with facet_grid
Expand Down Expand Up @@ -210,9 +215,14 @@
g5(2,3).stat_bin('geom','stairs') %Default fill is edges
g5(2,3).set_title('''stairs''')

figure
g5.set_title('''geom'' options for stat_bin()')
g5.draw()

figure('Position',[100 100 800 600])
g5.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/histograms_example','-dpng','-r0')
end

%%
% Example of alternative 'fill' options
Expand Down Expand Up @@ -243,6 +253,30 @@
g6.set_title('''fill'' options for stat_bin()')
g6.draw()


%% Those also work for different geoms

figure
clear g6
g6(1,1)=gramm('x',x,'color',cat)
g6(1,1).stat_bin('geom','line','fill','transparent')
g6(1,1).set_title('''transparent''')

g6(1,2)=gramm('x',x,'color',cat)
g6(1,2).stat_bin('geom','stairs','fill','transparent')
g6(1,2).set_title('''transparent''')

g6(2,1)=gramm('x',x,'color',cat)
g6(2,1).stat_bin('geom','line','fill','face')
g6(2,1).set_title('''face''')

g6(2,2)=gramm('x',x,'color',cat)
g6(2,2).stat_bin('geom','stairs','fill','all')
g6(2,2).set_title('''all''')

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

%%
% Examples of other histogram-generation options
%
Expand Down Expand Up @@ -309,8 +343,12 @@
%Set figure title
g.set_title('Fuel economy of new cars between 1970 and 1982')
% Do the actual drawing
g.draw()

figure('Position',[100 100 800 400])
g.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/carbig_example','-dpng','-r0')
end


%% Example from the readme (old)
Expand Down Expand Up @@ -339,9 +377,9 @@

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


figure
Expand All @@ -355,43 +393,57 @@
g.draw();


figure
figure('Position',[100 100 700 1000])
clear g
g(1,1)=gramm('x',catx,'y',y,'color',c);
g(1,1).stat_boxplot('spacing',0.5,'dodge',-1);
g(1,1).stat_boxplot();
g(1,1).geom_vline('xintercept',0.5:1:10.5,'style','k-');
g(1,1).set_title('''spacing'',0.5,''dodge'',-1')
g(1,1).set_title('''width'',0.6,''dodge'',0.7 (Default)')

g(2,1)=gramm('x',catx,'y',y,'color',c);
g(2,1).stat_boxplot('spacing',0.2,'dodge',0);
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('''spacing'',0.2,''dodge'',0')
g(2,1).set_title('''width'',0.5,''dodge'',0')

g(3,1)=gramm('x',catx,'y',y,'color',c);
g(3,1).stat_boxplot('spacing',0.2,'dodge',0.1);
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('''spacing'',0.5,''dodge'',0.1')
g(3,1).set_title('''width'',1,''dodge'',1')


g(4,1)=gramm('x',catx,'y',y,'color',c);
g(4,1).facet_grid([],c);
g(4,1).stat_boxplot('spacing',0.4,'dodge',-1);
g(4,1).set_title('''spacing'',0.4,''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)=gramm('x',catx,'y',y,'color',c);
g(5,1).facet_grid([],c);
g(5,1).stat_boxplot('width',0.5,'dodge',0);
g(5,1).set_title('''width'',0.5,''dodge'',0')
g.set_title('Dodge and spacing options for stat_boxplot()')
g.draw();


figure

figure('Position',[100 100 700 1000])
clear g
g(1,1)=gramm('x',catx,'y',y,'color',c);
g(1,1).stat_summary('geom',{'bar' 'black_errorbar'},'dodge',0);
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('''dodge'',0')
g(1,1).set_title('Default')

g(2,1)=gramm('x',catx,'y',y,'color',c);
g(2,1).stat_summary('geom',{'bar' 'black_errorbar'},'dodge',0.2);
g(2,1).set_title('''dodge'',0.2')
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)=gramm('x',catx,'y',y,'color',c);
g(3,1).stat_summary('geom',{'area'});
g(3,1).set_title('''geom'',''area''')

g(4,1)=gramm('x',catx,'y',y,'color',c);
g(4,1).stat_summary('geom',{'point' 'errorbar'},'dodge',0);
g(4,1).set_title('''dodge'',0')
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.set_title('Dodge options for stat_summary()')
g.draw();
Expand Down Expand Up @@ -433,7 +485,7 @@

load carbig.mat %Load example dataset about cars

figure
figure('Position',[100 100 600 450])


%We add another gramm plot (without color) to have a fit across all
Expand All @@ -447,62 +499,70 @@
g10.set_names('color','# Cylinders','x','Horsepower','y','Acceleration')
%g10.stat_glm('geom','area','disp_fit',true) %Linear fit (default for stat_glm
g10.geom_point()
g10.draw()
g10.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/carbig_glm_example','-dpng','-r0')
end



%% Colormap customization

load carbig.mat
clear g
figure

Origin=cellfun(@(c)strrep(c,' ',''),num2cell(Origin,2),'UniformOutput',false);

%Default: LCH-based colormap with hue variation
g(1,1)=gramm('x',Origin,'y',Horsepower,'color',Origin)
g(1,1).stat_summary('geom',{'bar'},'dodge',-1)
g(1,1).set_title('Default LCH colormap (''color'' groups)')
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)=gramm('x',Origin,'y',Horsepower,'color',Origin)
g(1,2).stat_summary('geom',{'bar'},'dodge',-1)
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 colormap (''color'' groups)')
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)=gramm('x',Origin,'y',Horsepower,'lightness',Origin)
g(1,3).stat_summary('geom',{'bar'},'dodge',-1)
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 colormap (''lightness'' groups)')
g(1,3).set_title('Modified LCH (''lightness'' groups)','FontSize',12)

%Go back to Matlab's defauls colormap
g(2,1)=gramm('x',Origin,'y',Horsepower,'color',Origin)
g(2,1).stat_summary('geom',{'bar'},'dodge',-1)
g(2,1).stat_summary('geom',{'bar'},'dodge',0)
g(2,1).set_color_options('map','matlab')
g(2,1).set_title('Matlab 2014B+ colormap')
g(2,1).set_title('Matlab 2014B+ ','FontSize',12)

%Brewer colormap 1
g(2,2)=gramm('x',Origin,'y',Horsepower,'color',Origin)
g(2,2).stat_summary('geom',{'bar'},'dodge',-1)
g(2,2).stat_summary('geom',{'bar'},'dodge',0)
g(2,2).set_color_options('map','brewer1')
g(2,2).set_title('brewer1 colormap')
g(2,2).set_title('Color Brewer 1','FontSize',12)

%Brewer colormap 2
g(2,3)=gramm('x',Origin,'y',Horsepower,'color',Origin)
g(2,3).stat_summary('geom',{'bar'},'dodge',-1)
g(2,3).stat_summary('geom',{'bar'},'dodge',0)
g(2,3).set_color_options('map','brewer2')
g(2,3).set_title('brewer2 colormap')
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')
g.draw()
figure('Position',[100 100 800 600])
g.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/colormaps_example','-dpng','-r0')
end

%% Example of all the different input formats for x and y

Expand Down Expand Up @@ -573,14 +633,18 @@

load spectra.mat

figure
%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;
g18.draw;
figure('Position',[100 100 600 450])
g18.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/continuous_color_example','-dpng','-r0')
end

%% Representation of 2D (bivariate) data

Expand Down Expand Up @@ -628,7 +692,12 @@
g(2,2).set_title('stat_bin2d(''geom'',''image'')')

g.set_title('Visualization of 2D densities')
g.draw()
figure('Position',[100 100 600 600])
g.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/2D_densities_example','-dpng','-r0')
end

%% stat_glm examples (statistics toolbox required)

Expand Down Expand Up @@ -681,13 +750,17 @@
y=y+randn(size(y))*1;

%Gramm plot with fit !
figure
clear g
g=gramm('x',x,'y',y,'color',cat)
g.geom_point()
g.stat_fit('fun',fun,'disp_fit',true) %We provide the function for the fit
g.set_title({'stat_fit() with user-provided function:' '@(alpha,beta,gamma,x)alpha*exp(cos(x-beta)*gamma)'})
g.draw()
figure('Position',[100 100 600 450])
g.draw();
if saveimg
set(gcf,'PaperPositionMode','auto')
print('img/fit_example','-dpng','-r0')
end

%% Changing the order of elements with set_order_options()

Expand All @@ -702,22 +775,22 @@
%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')
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')
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')
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
Expand All @@ -730,13 +803,14 @@
%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')
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])
g.draw()


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