Various small fixes

- Improved graphic fixes for old matlab versions
- Updated geom_abline() , geom_vbline(), geom_hbline() functions
- Bug fixes
- Added missing documentation

@gramm/draw.m

@@ -25,6 +25,20 @@
     end
 end
 
+%There are bugs with the hardware openGL renderer in pre 2014b version,
+%on Mac OS and Win the x and y axes become invisible and on
+%Windows the patch objects behave strangely.
+if ~obj(1).handle_graphics
+    if ismac
+        warning('Mac Pre-2014b version detected, forcing to ''Painters'' renderer to show axes lines. Use set(gcf,''Renderer'',''OpenGL'') to restore transparency')
+        if isprop(obj(1).parent,'Renderer')
+            set(obj(1).parent,'Renderer','Painters');
+        end
+    else
+        warning('Windows Pre-2014b version detected, forcing to software openGL which is less buggy')
+        opengl software
+    end
+end
 
 %Handle call of draw() on array of gramm objects by dividing the figure
 %up and launching the individual draw functions of each object
@@ -1174,15 +1188,25 @@
         %Set ablines, hlines and vlines (after axe properties in case the limits
         %are changed there
         if obj.abline.on
-            xl=get(ca,'xlim');
+            %xl=get(ca,'xlim');
             for line_ind=1:length(obj.abline.intercept)
+                tmp_xl=[obj.var_lim.minx obj.var_lim.maxx];
+                tmp_extent=(tmp_xl(2)-tmp_xl(1))*obj.abline.extent(line_ind)/2;
+                xl=[mean(tmp_xl)-tmp_extent mean(tmp_xl)+tmp_extent];
                 if ~isnan(obj.abline.intercept(line_ind))
                     %abline
                     plot(xl,xl*obj.abline.slope(line_ind)+obj.abline.intercept(line_ind),obj.abline.style{line_ind},'Parent',ca);
                 else
                     if ~isnan(obj.abline.xintercept(line_ind))
                         %vline
-                        yl=get(ca,'ylim');
+                        %yl=get(ca,'ylim');
+                        if obj.var_lim.miny == obj.var_lim.maxy %We are probably in a case where y wasn't provided (histogram or raster)
+                            tmp_yl=[0 numel(temp_aes.x)]; %We scale y according to number of x elements
+                        else
+                            tmp_yl=[obj.var_lim.miny obj.var_lim.maxy];
+                        end
+                        tmp_extent=(tmp_yl(2)-tmp_yl(1))*obj.abline.extent(line_ind)/2;
+                        yl=[mean(tmp_yl)-tmp_extent mean(tmp_yl)+tmp_extent];
                         plot([obj.abline.xintercept(line_ind) obj.abline.xintercept(line_ind)],yl,obj.abline.style{line_ind},'Parent',ca);
                     else
                         if ~isnan(obj.abline.yintercept(line_ind))
@@ -1232,14 +1256,6 @@
     obj.results=[];
 end
 
-%There are bugs with the openGL renderer in pre 2014b version,
-%on Mac OS and Win the x and y axes become invisible and on
-%Windows the patch objects behave strangely. So we switch to
-%painters renderer
-if verLessThan('matlab','8.4')
-    warning('Pre-2014b version detected, forcing to ''Painters'' renderer which is less buggy. Use set(gcf,''Renderer'',''OpenGL'') to restore transparency')
-    set(gcf,'Renderer','Painters')
-end
 
 obj.updater.first_draw=false;
 end

@gramm/geom_abline.m

@@ -12,9 +12,10 @@
 my_addParameter(p,'slope',1);
 my_addParameter(p,'intercept',0);
 my_addParameter(p,'style','k--');
+my_addParameter(p,'extent',2);
 parse(p,varargin{:});
 
 for obj_ind=1:numel(obj)
-    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,p.Results.slope,p.Results.intercept,NaN,NaN,@(x)x,p.Results.style);
+    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,p.Results.slope,p.Results.intercept,NaN,NaN,@(x)x,p.Results.style,p.Results.extent);
 end
 end

@gramm/geom_funline.m

@@ -8,9 +8,10 @@
 p=inputParser;
 my_addParameter(p,'fun',@(x)x);
 my_addParameter(p,'style','k--');
+my_addParameter(p,'extent',2);
 parse(p,varargin{:});
 
 for obj_ind=1:numel(obj)
-    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,NaN,NaN,NaN,NaN,p.Results.fun,p.Results.style);
+    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,NaN,NaN,NaN,NaN,p.Results.fun,p.Results.style,p.Results.extent);
 end
 end

@gramm/geom_hline.m

@@ -7,9 +7,10 @@
 p=inputParser;
 my_addParameter(p,'yintercept',0);
 my_addParameter(p,'style','k--');
+my_addParameter(p,'extent',2);
 parse(p,varargin{:});
 
 for obj_ind=1:numel(obj)
-    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,NaN,NaN,NaN,p.Results.yintercept,@(x)x,p.Results.style);
+    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,NaN,NaN,NaN,p.Results.yintercept,@(x)x,p.Results.style,p.Results.extent);
 end
 end

@gramm/geom_label.m

@@ -1,14 +1,14 @@
 function obj = geom_label(obj,varargin)
 % geom_label Display data as labels
 %
-% Example syntax: gramm_object.geom_jitter('Color','auto','dodge',0.6)
+% Example syntax: gramm_object.geom_label('Color','auto','dodge',0.6)
 % Geom label displays text (provided as 'label' in the constructor call
 % gramm()). At the X and Y locations provided in the constructor call.
 % Appearance of the text can be customized with any text property given as
 % 'name',value pair in the arguments. The color-related arguments
 % ('Color','EdgeColor','BackgroundColor') can also be set to 'auto' in
 % order for the corresponding element to be colored according the the
-% colro groups provided in the constructor. geom_label() also accepts a
+% color groups provided in the constructor. geom_label() also accepts a
 % 'dodge' argument.
 
 

@gramm/geom_vline.m

@@ -7,9 +7,10 @@
 p=inputParser;
 my_addParameter(p,'xintercept',0);
 my_addParameter(p,'style','k--');
+my_addParameter(p,'extent',2);
 parse(p,varargin{:});
 
 for obj_ind=1:numel(obj)
-    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,NaN,NaN,p.Results.xintercept,NaN,@(x)x,p.Results.style);
+    obj(obj_ind).abline=fill_abline(obj(obj_ind).abline,NaN,NaN,p.Results.xintercept,NaN,@(x)x,p.Results.style,p.Results.extent);
 end
 end

@gramm/gramm.m

@@ -69,7 +69,8 @@
             'xintercept',[],...
             'yintercept',[],...
             'style',[],...
-            'fun',[])
+            'fun',[],...
+            'extent',[])
 
         datetick_params={} %cell containng datetick parameters
         current_row %What is the currently drawn row of the subplot

@gramm/private/fill_abline.m

@@ -6,6 +6,7 @@
 ab.intercept(end+1:end+l)=shiftdim(varargin{2});
 ab.xintercept(end+1:end+l)=shiftdim(varargin{3});
 ab.yintercept(end+1:end+l)=shiftdim(varargin{4});
+ab.extent(end+1:end+l)=shiftdim(varargin{7});
 
 %Because of the constructor these are initialized as empty
 %arrays

@gramm/set_text_options.m

@@ -3,6 +3,7 @@
 %
 % 'name',value pairs:
 % 'base_size': Base text size, corresponds to axis ticks text size (default is 10)
+% 'interpreter': 'none'(default), 'tex' or 'latex'
 % 'label_scaling': Scaling of axis label sizes relative to base (default is 1)
 % 'legend_scaling': Scaling of legend label sizes relative to base (default is 1)
 % 'legend_title_scaling': Scaling of legend title sizes relative to base (default is 1.2)

@gramm/stat_ellipse.m

@@ -118,8 +118,10 @@
         m=nanmean(r);
         cv=nancov(r);
 
-        obj.results.ellipse{obj.result_ind,1}.mean=m;
-        obj.results.ellipse{obj.result_ind,1}.cv=cv;
+        obj.results.stat_ellipse{obj.result_ind,1}.mean=m;
+        obj.results.stat_ellipse{obj.result_ind,1}.cv=cv;
+        obj.results.stat_ellipse{obj.result_ind,1}.major_axis=[];
+        obj.results.stat_ellipse{obj.result_ind,1}.minor_axis=[];
 
         conf_sphpoints=sphpoints;
         conf_sphpoints.vertices=bsxfun(@plus,sqrtm(cv)*conf_sphpoints.vertices'*k(obj.stat_options.alpha),m')';
@@ -131,5 +133,12 @@
     obj.results.stat_ellipse{obj.result_ind,1}.center_handle=center_hndl;
 else
     warning('Not enough points for ellipse')
+
+    obj.results.stat_ellipse{obj.result_ind,1}.mean=NaN;
+    obj.results.stat_ellipse{obj.result_ind,1}.cv=NaN;
+    obj.results.stat_ellipse{obj.result_ind,1}.major_axis=[];
+    obj.results.stat_ellipse{obj.result_ind,1}.minor_axis=[];
+    obj.results.stat_ellipse{obj.result_ind,1}.ellipse_handle=[];
+    obj.results.stat_ellipse{obj.result_ind,1}.center_handle=[];
 end
 end

@gramm/stat_summary.m

@@ -19,9 +19,18 @@
 %       percentiles
 %       - '95percentile': display the median and 2.5 and 97.5
 %       percentiles
-%        - 'fitnormalci'
+%       - 'fitnormalci'
 %       - 'fitpoissonci'
-%        - 'fit95percentile'
+%       - 'fit95percentile'
+%       - @function : provide a the handle to a custom function that takes 
+%       y values (as an n_repetitions x n_data_points matrix) and returns 
+%       both the central value and the CI with a matrix [y_central ; yc_CI_low ; y_CI_high]
+%       (with y_central, and y_CIs being 1 x n_data_points arrays).
+%       Example that uses the trimmed mean instead of regular mean:
+%
+%       custom_statfun = @(y)([trimmean(y,2.5);bootci(500,{@(ty)trimmean(ty,2.5),y},'alpha',0.05)]); 
+%       gramm_object.stat_summary('type', custom_statfun)
+%
 % - 'geom':
 %       - 'line': displays a line that connects the central locations
 %       (mean,median)