Directly draw confidence intervals, improved dodging

- User-provided confidence intervals can now be represented with
geom_interval()
- Improved dodging: now takes in account the number of colors per x
value
- Dodging supported in geom_point(), geom_line(), geom_jitter(),
geom_bar()
- Improved geom_bar() stacking

@gramm/draw.m

@@ -76,22 +76,9 @@
     return
 end
 
-temp_aes=validate_aes(obj.aes);
+obj.aes=validate_aes(obj.aes);
 
-% Create replacement row_facet and color_facet if they were
-% empty
-if isempty(obj.row_facet)
-    obj.row_facet=ones(size(temp_aes.subset));
-end
-
-if isempty(obj.col_facet)
-    obj.col_facet=ones(size(temp_aes.subset));
-end
-
-temp_row_facet=obj.row_facet(temp_aes.subset);
-temp_col_facet=obj.col_facet(temp_aes.subset);
-
-temp_aes=select_aes(temp_aes,temp_aes.subset);
+temp_aes=select_aes(obj.aes,obj.aes.subset);
 
 %Find min and max of x and y to have homogenous scales
 nonemptycell=@(c)~cellfun(@isempty,c);
@@ -126,14 +113,23 @@
     obj.var_lim.minx=min(min(temp_aes.x));
 end
 
+%Depending on whether ymin of ymax are present we change what to pick for
+%limit computation
+if ~isempty(temp_aes.ymin) && ~isempty(temp_aes.ymax)
+    tmp_y_for_min=temp_aes.ymin;
+    tmp_y_for_max=temp_aes.ymax;
+else
+    tmp_y_for_min=temp_aes.y;
+    tmp_y_for_max=temp_aes.y;
+end
+
 if iscell(temp_aes.y)
     nonempty=nonempty & nonemptycell(temp_aes.y);
-
-    obj.var_lim.maxy=cellmax(temp_aes.y);
-    obj.var_lim.miny=cellmin(temp_aes.y);
+    obj.var_lim.maxy=cellmax(tmp_y_for_max);
+    obj.var_lim.miny=cellmin(tmp_y_for_min);
 else
-    obj.var_lim.maxy=max(max(temp_aes.y));
-    obj.var_lim.miny=min(min(temp_aes.y));
+    obj.var_lim.maxy=max(max(tmp_y_for_max));
+    obj.var_lim.miny=min(min(tmp_y_for_min));
 end
 
 if ~isempty(temp_aes.z)
@@ -149,8 +145,6 @@
 end
 
 temp_aes=select_aes(temp_aes,nonempty);
-temp_row_facet=temp_row_facet(nonempty);
-temp_col_facet=temp_col_facet(nonempty);
 
 %Handles the multiple gramm case: we set up subtightplot so
 %that it restricts the drawing (using margins) to a portion of
@@ -171,8 +165,8 @@
 mysubplot_wrap=@(ncol,col)mysubtightplot(ceil(ncol/obj.wrap_ncols),obj.wrap_ncols,col,[0.09 0.03],[0.1 0.2],[0.1 0.2]);
 
 %Find uniques in aesthetics and sort according to options
-uni_row=unique_and_sort(temp_row_facet,obj.order_options.row);
-uni_column=unique_and_sort(temp_col_facet,obj.order_options.column);
+uni_row=unique_and_sort(temp_aes.row,obj.order_options.row);
+uni_column=unique_and_sort(temp_aes.column,obj.order_options.column);
 uni_linestyle=unique_and_sort(temp_aes.linestyle,obj.order_options.linestyle);
 uni_marker=unique_and_sort(temp_aes.marker,obj.order_options.marker);
 uni_lightness=unique_and_sort(temp_aes.lightness,obj.order_options.lightness);
@@ -218,12 +212,12 @@
     uni_marker=num2cell(uni_marker);
 end
 
-%Correct empty facet_grids
+%Correct empty facets when wrapping
 if obj.wrap_ncols>length(uni_column)
     obj.wrap_ncols=length(uni_column);
 end
 
-%The plot minumums and maximums arrays the size of the
+%The plot minimums and maximums arrays the size of the
 %number of subplots
 n_columns=length(uni_column);
 n_rows=length(uni_row);
@@ -271,27 +265,34 @@
 %Index in the loops
 obj.result_ind=1;
 
+%Initialize facet axes handles
 if obj.updater.first_draw
-    if obj.handle_graphics
+    if obj.handle_graphics %Post 2014b we return objects
         obj.facet_axes_handles=gobjects(length(uni_row),length(uni_column));
     else
         obj.facet_axes_handles=zeros(length(uni_row),length(uni_column));
     end
 end
 
+%Set the dodge width across all facets
+draw_data.dodge_avl_w=min(diff(unique(comb(temp_aes.x))));
+if isempty(draw_data.dodge_avl_w) || draw_data.dodge_avl_w==0
+    draw_data.dodge_avl_w=1;
+end
+
 
 %% draw() looping
 %Loop over rows
 for ind_row=1:length(uni_row)
 
-    sel_row=multi_sel(temp_row_facet,uni_row{ind_row});
+    sel_row=multi_sel(temp_aes.row,uni_row{ind_row});
 
     obj.current_row=ind_row;
 
     %Loop over columns
     for ind_column=1:length(uni_column)
 
-        sel_column=sel_row & multi_sel(temp_col_facet,uni_column{ind_column});
+        sel_column=sel_row & multi_sel(temp_aes.column,uni_column{ind_column});
 
         obj.current_column=ind_column;
 
@@ -311,14 +312,14 @@
                     obj.plot_lim.minx(obj.current_row,obj.current_column));
             end
             if iscell(temp_aes.y(sel_column))
-                obj.plot_lim.maxy(obj.current_row,obj.current_column)=max(cellmax(temp_aes.y(sel_column)),...
+                obj.plot_lim.maxy(obj.current_row,obj.current_column)=max(cellmax(tmp_y_for_max(sel_column)),...
                     obj.plot_lim.maxy(obj.current_row,obj.current_column));
-                obj.plot_lim.miny(obj.current_row,obj.current_column)=min(cellmin(temp_aes.y(sel_column)),...
+                obj.plot_lim.miny(obj.current_row,obj.current_column)=min(cellmin(tmp_y_for_min(sel_column)),...
                     obj.plot_lim.miny(obj.current_row,obj.current_column));
             else
-                obj.plot_lim.maxy(obj.current_row,obj.current_column)=max(max(temp_aes.y(sel_column)),...
+                obj.plot_lim.maxy(obj.current_row,obj.current_column)=max(max(tmp_y_for_max(sel_column)),...
                     obj.plot_lim.maxy(obj.current_row,obj.current_column));
-                obj.plot_lim.miny(obj.current_row,obj.current_column)=min(min(temp_aes.y(sel_column)),...
+                obj.plot_lim.miny(obj.current_row,obj.current_column)=min(min(tmp_y_for_min(sel_column)),...
                     obj.plot_lim.miny(obj.current_row,obj.current_column));
             end
             if ~isempty(temp_aes.z)
@@ -400,6 +401,9 @@
         %missing data).
         draw_data.facet_x=temp_aes.x(sel_column);
 
+        %Store data for advanced dodging
+        [dodge_data.fallback,dodge_data.x,dodge_data.color,dodge_data.lightness,dodge_data.ind,dodge_data.n]=dodge_comp(temp_aes.x(sel_column),temp_aes.color(sel_column),temp_aes.lightness(sel_column),uni_color,uni_lightness);
+
         %Loop over point shapes
         for ind_marker=1:length(uni_marker)
 
@@ -435,6 +439,19 @@
                                 uni_group=num2cell(uni_group);
                             end
 
+                            %Select dodging parameters for current color
+                            %and lightness
+                            if obj.continuous_color
+                                sel_dodge=true(size(dodge_data.color));
+                            else
+                                sel_dodge=multi_sel(dodge_data.color,uni_color{ind_color}) & multi_sel(dodge_data.lightness,uni_lightness{ind_lightness});
+                            end
+
+                            draw_data.dodge_fallback=dodge_data.fallback;
+                            draw_data.dodge_x=dodge_data.x(sel_dodge);
+                            draw_data.dodge_ind=dodge_data.ind(sel_dodge);
+                            draw_data.dodge_n=dodge_data.n(sel_dodge);
+
                             %Loop over groups
                             for ind_group=1:length(uni_group)
 
@@ -468,6 +485,13 @@
                                     %individual geoms
                                     draw_data.x=temp_aes.x(sel);
                                     draw_data.y=temp_aes.y(sel);
+                                    if ~isempty(temp_aes.ymin) && ~isempty(temp_aes.ymax)
+                                        draw_data.ymin=temp_aes.ymin(sel);
+                                        draw_data.ymax=temp_aes.ymax(sel);
+                                    else
+                                        draw_data.ymin=[];
+                                        draw_data.ymax=[];
+                                    end
                                     if ~isempty(temp_aes.z)
                                         draw_data.z=temp_aes.z(sel);
                                     else

@gramm/facet_grid.m

@@ -39,8 +39,8 @@
 
 %Handle case where facet_grid is called after update()
 if obj.updater.updated
-    if isnumeric(obj.row_facet) && isnumeric(obj.col_facet) && all(obj.row_facet==1) && all(obj.col_facet==1)
-        if isempty(obj.row_facet) && isempty(obj.col_facet)
+    if isnumeric(obj.aes.row) && isnumeric(obj.aes.column) && all(obj.aes.row==1) && all(obj.aes.column==1)
+        if isempty(obj.aes.row) && isempty(obj.aes.column)
             %User probably tried to update all the data
             obj.updater.facet_updated=0;
         else
@@ -57,15 +57,8 @@
     end
 end
 
-if iscategorical(row)
-    obj.row_facet=shiftdim(cellstr(row));
-else
-    obj.row_facet=shiftdim(row);
-end
-if iscategorical(col)
-    obj.col_facet=shiftdim(cellstr(col));
-else
-    obj.col_facet=shiftdim(col);
-end
+obj.aes.row=shiftdim(row);
+obj.aes.column=shiftdim(col);
+
 obj.wrap_ncols=-1;
 end

@gramm/facet_wrap.m

@@ -23,8 +23,8 @@
 
 %Handle case where facet_wrap is called after update()
 if obj.updater.updated
-    if isnumeric(obj.row_facet) && isnumeric(obj.col_facet) && all(obj.row_facet==1) && all(obj.col_facet==1)
-        if isempty(obj.row_facet) && isempty(obj.col_facet)
+    if isnumeric(obj.aes.row) && isnumeric(obj.aes.column) && all(obj.aes.row==1) && all(obj.aes.column==1)
+        if isempty(obj.aes.row) && isempty(obj.aes.column)
             %User probably tried to update all the data
             obj.updater.facet_updated=0;
         else
@@ -42,10 +42,7 @@
 end
 
 obj.wrap_ncols=p.Results.ncols;
-if iscategorical(col)
-    obj.col_facet=shiftdim(cellstr(col));
-else
-    obj.col_facet=shiftdim(col);
-end
-obj.row_facet=[];
+obj.aes.column=shiftdim(col);
+obj.aes.row=[];
+
 end

@gramm/geom_bar.m

@@ -10,6 +10,7 @@
 p=inputParser;
 my_addParameter(p,'width',0.80);
 my_addParameter(p,'stacked',false);
+my_addParameter(p,'dodge',0);
 parse(p,varargin{:});
 
 obj.geom=vertcat(obj.geom,{@(dd)my_bar(obj,dd,p.Results)});
@@ -31,33 +32,33 @@
 
     %Problem with stacked bar when different x values are used
     if obj.firstrun(obj.current_row,obj.current_column)
-        obj.extra.stacked_bar_height=zeros(1,length(x));
+        %Store heights at the level of dodge x
+        obj.extra.stacked_bar_height=zeros(1,length(draw_data.dodge_x));
         obj.plot_lim.minx(obj.current_row,obj.current_column)=min(x)-width;
         obj.plot_lim.maxx(obj.current_row,obj.current_column)=max(x)+width;
         %obj.firstrun(obj.current_row,obj.current_column)=0;
     end
 
+    x_stack_ind=arrayfun(@(xin)find(abs(draw_data.dodge_x-xin)<1e-10,1),x);
+
     hndl=patch([x-width/2 ; x+width/2 ; x+width/2 ; x-width/2],...
-        [obj.extra.stacked_bar_height ; obj.extra.stacked_bar_height ; obj.extra.stacked_bar_height+y ; obj.extra.stacked_bar_height+y],...
+        [obj.extra.stacked_bar_height(x_stack_ind) ; obj.extra.stacked_bar_height(x_stack_ind) ; obj.extra.stacked_bar_height(x_stack_ind)+y ; obj.extra.stacked_bar_height(x_stack_ind)+y],...
         draw_data.color,'EdgeColor','k');
 
-    obj.extra.stacked_bar_height=obj.extra.stacked_bar_height+y;
+    obj.results.geom_bar_handle{obj.result_ind,1}=hndl;
 
+    obj.extra.stacked_bar_height(x_stack_ind)=obj.extra.stacked_bar_height(x_stack_ind)+y;
     if obj.plot_lim.maxy(obj.current_row,obj.current_column)<max(obj.extra.stacked_bar_height)
         obj.plot_lim.maxy(obj.current_row,obj.current_column)=max(obj.extra.stacked_bar_height);
     end
 
 else
 
-    if min(x+(draw_data.color_index/(draw_data.n_colors+1)-0.5)*width-width/(draw_data.n_colors+1))<obj.plot_lim.minx(obj.current_row,obj.current_column)
-        obj.plot_lim.minx(obj.current_row,obj.current_column)=min((draw_data.color_index/(draw_data.n_colors+1)-0.5)*width-width/(draw_data.n_colors+1));
-    end
-    if max(x+(draw_data.color_index/(draw_data.n_colors+1)-0.5)*width+width/(draw_data.n_colors+1))>obj.plot_lim.maxx(obj.current_row,obj.current_column)
-        obj.plot_lim.maxx(obj.current_row,obj.current_column)=max(x+(draw_data.color_index/(draw_data.n_colors+1)-0.5)*width+width/(draw_data.n_colors+1));
-    end
+
+    hndl=plotci(obj,x,y,[y y],draw_data,'edge_bar',params.dodge,params.width);
+    obj.results.geom_bar_handle{obj.result_ind,1}=hndl.bar_handle;
 
-    hndl=bar(x+(draw_data.color_index/(draw_data.n_colors+1)-0.5)*width,y,width/(draw_data.n_colors+1),'faceColor',draw_data.color,'EdgeColor','none');
 end
 
-obj.results.geom_bar_handle{obj.result_ind,1}=hndl;
+
 end

@gramm/geom_interval.m

@@ -0,0 +1,47 @@
+function obj = geom_interval( obj,varargin )
+
+p=inputParser;
+my_addParameter(p,'geom','area');
+my_addParameter(p,'dodge',[]);
+my_addParameter(p,'width',[]);
+parse(p,varargin{:});
+
+obj.geom=vertcat(obj.geom,{@(dd)my_ci(obj,dd,p.Results)});
+obj.results.geom_interval={};
+
+end
+
+function hndl=my_ci(obj,draw_data,params)
+
+if isempty(draw_data.ymin) || isempty(draw_data.ymax)
+    error('No ymin or ymax data for geom_ci');
+end
+
+%Advanced defaults
+if isempty(params.dodge)
+    if sum(strcmp(params.geom,'bar'))>0 && draw_data.n_colors>1 %If we have a bar as geom, we dodge
+        params.dodge=0.6;
+    else
+        params.dodge=0;
+    end
+end
+
+if isempty(params.width) %If no width given
+    if params.dodge>0 %Equal to dodge if dodge given
+        params.width=params.dodge*0.8;
+    else
+        params.width=0.5;
+    end
+end
+
+if iscell(draw_data.x)
+    for k=1:length(draw_data.x)
+        plotci(obj,draw_data.x{k},draw_data.y{k},[draw_data.ymin{k} draw_data.ymax{k}],draw_data,params.geom,params.dodge,params.width);
+    end
+else
+    hndl=plotci(obj,draw_data.x,draw_data.y,[draw_data.ymin draw_data.ymax],draw_data,params.geom,params.dodge,params.width);
+end
+
+obj.results.geom_interval{obj.result_ind,1}=hndl;
+
+end

@gramm/geom_jitter.m

@@ -9,6 +9,7 @@
 p=inputParser;
 my_addParameter(p,'width',0.2);
 my_addParameter(p,'height',0.2);
+my_addParameter(p,'dodge',0);
 parse(p,varargin{:});
 
 obj.geom=vertcat(obj.geom,{@(dd)my_jitter(obj,dd,p.Results)});
@@ -18,6 +19,8 @@
 
 function  hndl=my_jitter(obj,draw_data,params)
 
+draw_data.x=dodger(draw_data.x,draw_data,params.dodge);
+
 draw_data.x=draw_data.x+rand(size(draw_data.x))*params.width-params.width/2;
 draw_data.y=draw_data.y+rand(size(draw_data.y))*params.height-params.height/2;