plotting advanced

statistics/lecture_statistics.tex

@@ -113,7 +113,7 @@ Bernstein Center T\"ubingen}
 % PCA
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section[Präludium]{Prelude}
+\section[Prelude]{Prelude}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % ----------------------------------------------------------
@@ -364,32 +364,162 @@ correlation coefficient does not have that property.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %-------------------------------------------------------------
 \begin{frame}[fragile]
-  \frametitle{Darstellung nominaler Daten}
+  \frametitle{}
-  \framesubtitle{Bar-Plot f\"ur Anzahl/ rel. H\"aufigkeit}
+  \begin{center}
+    \Huge What makes a good plot?
+  \end{center}
+\end{frame}
+
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{features of a good plot}
+  A good plot
+  \begin{itemize}
+  \item helps the reader to clearly understand your point.\pause
+  \item is not misleading and let's the reader judge the information
+    on her own (different y-axis/length scales in two related plots,
+    "squeezing" via log-plots). \pause
+  \item contains information about the data (a comic might be
+    illustrative, but does not contain information about the
+    data).\pause
+  \item adheres to the principle of {\em ink minimization}.
+  \end{itemize}
+\end{frame}
+
+
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{features of a good plot}
+  \framesubtitle{design/organization}
+  \begin{itemize}
+  \item Is the display consistent with the model or hypothesis
+    being tested?\pause
+  \item Are there "empty dimensions" in the display that could be
+    removed (A 3D pie chart for 2D categorical data, extraneous colors
+    that do not encode meaningful information)?\pause
+  \item Does the display provide an honest and transparent portrayal
+    of the data (hiding, smoothing, modifying data points should be
+    avoided or explicitly mentioned)?
+  \end{itemize}
+  \mycite{Allen et al. 2012, Neuron}
+\end{frame}
+
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{features of a good plot}
+  \framesubtitle{axes}
+  \begin{itemize}
+  \item Are axes scales defined as linear, log, or radial?\pause
+  \item Does each axis label describe the variable and its units (use
+    "a.u." for arbitrary units)?\pause
+  \item Are axes limits appropriate for the data (The graphic should
+    not be bounded at zero if the data can take on both positive and
+    negative values.)?\pause
+  \item Is the aspect ratio appropriate for the data (When x and y
+    axes contrast the same variable under different conditions the
+    graphic should be square.)?
+  \end{itemize}
+  \mycite{Allen et al. 2012, Neuron}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{features of a good plot}
+  \framesubtitle{color mapping}
+  \begin{itemize}
+  \item Is a color bar provided?\pause
+  \item Is the color map sensible for the data type (does the data
+    extend to both $\pm$, does it live in an interval, is it
+    circular)?\pause
+  \item Are contrasting colors consistent with a natural interpretation?
+  \item Can features be discriminated when printed in grayscale?
+  \item Has red/green contrast been avoided to accommodate common
+    forms of colorblindness?
+  \end{itemize}
+  \mycite{Allen et al. 2012, Neuron}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{features of a good plot}
+  \framesubtitle{uncertainty}
+  \begin{itemize}
+  \item Does the display indicate the uncertainty of estimated parameters?\pause
+  \item Is the type of error surface appropriate for the data?
+    \begin{itemize}
+    \item Use standard deviations to describe variability in the population.\pause
+    \item Use standard errors or confidence intervals to make inferences
+      about parameters estimated from a sample.\pause
+    \item Parametric confidence intervals should only be used if data
+      meet the assumptions of the underlying model.\pause
+    \end{itemize}
+  \item Are the units of uncertainty defined (is it standard error, is
+    it $95\%$ confidence interval)?
+  \end{itemize}
+  \mycite{Allen et al. 2012, Neuron}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{features of a good plot}
+  \framesubtitle{annotation}
+  \begin{itemize}
+  \item Are all symbols defined, preferably by directly labeling objects?\pause
+  \item Is the directionality of a contrast between conditions obvious?\pause
+  \item Is the number of samples or independent experiments indicated?\pause
+  \item Are statistical procedures and criteria for significance described?\pause
+  \item Are uncommon abbreviations avoided or clearly defined?\pause
+  \item Are abbreviations consistent with those used in the text?
+  \end{itemize}
+  \mycite{Allen et al. 2012, Neuron}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{suboptimal example}
+      \begin{center}
+        \includegraphics[width=.5\linewidth]{figs/nobelbad}
+      \end{center}
+      \mycite{Hafting et al. 2005, nature}
+\end{frame}
+
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{different axes}
+\end{frame}
+%-------------------------------------------------------------
+
+\begin{frame}
+  \frametitle{Bad bar plot}
+  \begin{center}
+    \includegraphics[width=.8\linewidth]{figs/badbarplot}
+  \end{center}
+  \source{www.enfovis.com}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{plotting nominal data}
+  \framesubtitle{bar plot for count and relative frequency}
       \begin{center}
         \includegraphics[width=.8\linewidth]{figs/nominaldataplot}
       \end{center}
 \end{frame}
 %-------------------------------------------------------------
 \begin{frame}[fragile]
-  \frametitle{Darstellung nominaler Daten}
+  \frametitle{plotting nominal data}
-  \framesubtitle{Bar-Plot f\"ur Anzahl/ rel. H\"aufigkeit}
+  \framesubtitle{bar plot for count and relative frequency}
       \scriptsize
 \begin{lstlisting}
-% eigentlicher Plot
+% plot
 bar([1,2], [50, 90], 'facecolor', 'k')
 
-% Achsenbeschriftung
+% labels axes
 ylabel('cell count')
 xlabel('cell type')
 
-% Kosmetik
+% cosmetics
 xlim([0.5,2.5])
 ylim([0, 100])
 box('off')
 set(gca,'XTick',1:2,'XTickLabel',{'pyramidal','interneuron'},'FontSize',20)
 
-% Settings fuers Abspeichern
+% settings for saving the figure
 set(gcf, 'PaperUnits', 'centimeters');
 set(gcf, 'PaperSize', [11.7 9.0]);
 set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
@@ -398,8 +528,8 @@ set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
 
 %----------------------------------------------------------
 \begin{frame}[fragile]
-  \frametitle{Darstellung nominaler Daten}
+  \frametitle{plotting nominal data}
-  \framesubtitle{Pie-Chart f\"ur Anzahl/ rel. H\"aufigkeit}
+  \framesubtitle{pie chart for count and relative frequency}
       \begin{center}
         \includegraphics[width=.8\linewidth]{figs/nominaldataplot2}
       \end{center}
@@ -407,15 +537,15 @@ set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
 %-------------------------------------------------------------
 \begin{frame}[fragile]
   \frametitle{Darstellung nominaler Daten}
-  \framesubtitle{\"Ubung}
+  \framesubtitle{exercise}
-  \begin{task}{Pie-Chart}
+  \begin{task}{pie chart}
-    Plotte dieselben Daten ($n_{py}=50$, $n_{in}=90$) als Pie-Chart in Matlab.
+    Plot the same data ($n_{py}=50$, $n_{in}=90$) as a pie chart in Matlab.
   \end{task}
 \end{frame}
 %-------------------------------------------------------------
 \begin{frame}[fragile]
   \frametitle{Darstellung nominaler Daten}
-  \framesubtitle{Pie-Chart f\"ur Anzahl/ rel. H\"aufigkeit}
+  \framesubtitle{pie chart for relative frequency}
       \scriptsize
 \begin{lstlisting}
 data = [50, 90];
@@ -438,10 +568,65 @@ set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
 
 %-------------------------------------------------------------
 \begin{frame}[fragile]
-  \frametitle{Darstellung von Interval-/Absolutskala Daten}
+  \frametitle{plotting interval/ratio/absolute data}
+  \framesubtitle{histogram}
+      \begin{center}
+        \includegraphics[width=.8\linewidth]{figs/histogram}
+      \end{center}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{plotting interval/ratio/absolute data}
+  \framesubtitle{bad choice of bins}
+      \begin{center}
+        \includegraphics[width=.4\linewidth]{figs/histogrambad}
+        \includegraphics[width=.4\linewidth]{figs/histogrambad2}
+      \end{center}
+      \begin{summary}{Rule of thumb}
+        Choose the bins $b\approx n/20$.
+      \end{summary}
+\end{frame}
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{plotting interval/ratio/absolute data}
+  \framesubtitle{how to do in Matlab}
+      \scriptsize
+\begin{lstlisting}
+x = randn(2000,1); % generate Gaussian data
+
+hist(x, 50); % generate histogram
+
+% set facecolor to gray
+h = findobj(gca, 'Type','patch');
+set(h(1), 'FaceColor',[.2,.2,.2], 'EdgeColor','w', 'linewidth',2)
 
+% plot a white grid over it
+h = gridxy([],get(gca,'ytick'),'color','w','linewidth',2)
+uistack(h, 'top')
+
+% cosmetics
+box('off');
+xlabel('Data')
+ylabel('Count')
+\end{lstlisting}
 \end{frame}
 
+%-------------------------------------------------------------
+\begin{frame}[fragile]
+  \frametitle{plotting interval/ratio/absolute data}
+  \framesubtitle{other ways}
+  There are other ways to plot a sample $x_1, ..., x_n$ of
+  interval/ratio/absolute scale data. E.g. 
+  \begin{itemize}
+  \item box plot 
+  \item bar plot
+  \item smoothed histogram
+  \item ...
+  \end{itemize}
+  We will look at them while plotting mixed data in the following.
+\end{frame}
+
+
 \end{document} 
  
  

statistics/matlab/gridxy.m

@@ -0,0 +1,127 @@
+function hh = gridxy(x,varargin)
+% GRIDXY - Plot grid lines
+%   GRIDXY(X) plots vertical grid lines at the positions specified
+%   by X. GRIDXY(X,Y) also plots horizontal grid lines at the positions
+%   specified by Y. GRIDXY uses the current axes, if any. Lines outside
+%   the plot area are plotted but not shown. When X or Y is empty no vertical
+%   or horizontal lines are plotted.
+%
+%   The lines are plotted as a single graphics object. H = GRIDXY(..) returns
+%   a graphics handle to that line object. 
+%
+%   GRIDXY(..., 'Prop1','Val1','Prop2','Val2', ...) uses the properties
+%   and values specified for color, linestyle, etc. Execute GET(H), where H is
+%   a line handle, to see a list of line object properties and their current values.
+%   Execute SET(H) to see a list of line object properties and legal property values.
+%
+%   Examples
+%     % some random plot
+%       plot(10*rand(100,1), 10*rand(100,1),'bo') ; 
+%     % horizontal red dashed grid
+%       gridxy([1.1 3.2 4.5],'Color','r','Linestyle',':') ;
+%     % vertical solid thicker yellowish grid, and store the handle
+%       h = gridxy([],[2.1:0.7:5 8],'Color',[0.9 1.0 0.2],'linewidth',3) ;
+%
+%   GRIDXY can be used to plot a irregular grid on the axes.
+%
+%   See also PLOT, REFLINE, GRID, AXES, REFLINEXY
+
+% NOTE: This function was previously known as XYREFLINE
+
+% for Matlab R13
+% version 2.2 (feb 2008)
+% (c) Jos van der Geest
+% email: jos@jasen.nl
+
+% History
+% Created (1.0) feb 2006
+% 2.0 apr 2007 - renamed from reflinexy to gridxy, reflinexy is now used
+%               for plotting intersection between X and Y axes
+% 2.1 apr 2007 - add error check for line properties
+% 2.2 feb 2008 - added set(gca,'layer','top') to put gridlines behind the
+%                axis tick marks
+
+error(nargchk(1,Inf,nargin)) ;
+
+% check the arguments
+if ~isnumeric(x),
+    error('Numeric argument expected') ;
+end
+
+if nargin==1,
+    y = [] ;
+    va = [] ;
+else
+    va = varargin ;
+    if ischar(va{1}),
+        % optional arguments are
+        y = [] ;
+    elseif isnumeric(va{1})        
+        y = va{1} ;
+        va = va(2:end) ;
+    else
+        error('Invalid second argument') ;
+    end
+    if mod(size(va),2) == 1,
+        error('Property-Value have to be pairs') ;
+    end
+end
+
+% get the axes to plot in
+hca=get(get(0,'currentfigure'),'currentaxes');
+if isempty(hca),
+    warning('No current axes found') ;
+    return ;
+end
+
+% get the current limits of the axis
+% used for limit restoration later on
+xlim = get(hca,'xlim') ;
+ylim = get(hca,'ylim') ;
+
+% setup data for the vertical lines
+xx1 = repmat(x(:).',3,1) ;
+yy1 = repmat([ylim(:) ; nan],1,numel(x)) ;
+
+% setup data for the horizontal lines
+xx2 = repmat([xlim(:) ; nan],1,numel(y)) ;
+yy2 = repmat(y(:).',3,1) ;
+
+
+% create data for a single line object
+xx1 = [xx1 xx2] ;
+if ~isempty(xx1),     
+    yy1 = [yy1 yy2] ;
+    % add the line to the current axes
+    np = get(hca,'nextplot') ;
+    set(hca,'nextplot','add') ;
+    h = line('xdata',xx1(:),'ydata',yy1(:)) ;          
+    set(hca,'ylim',ylim,'xlim',xlim) ; % reset the limits
+    
+    uistack(h,'bottom') ; % push lines to the bottom of the graph
+    set(hca,'nextplot',np,'Layer','top') ;    % reset the nextplot state
+
+    if ~isempty(va),
+        try
+            set(h,va{:}) ; % set line properties        
+        catch
+            msg = lasterror ;
+            error(msg.message(21:end)) ;
+        end
+    end
+
+else
+    h = [] ;
+end
+
+if nargout==1,     % if requested return handle
+    hh = h ;
+end
+
+
+
+
+
+
+
+

statistics/matlab/intervalplots.m

@@ -2,5 +2,15 @@ close all
 % histogram
 figure()
 x = randn(2000,1);
-hist(x, 50, 'gray')
+hist(x, 50);
+h = findobj(gca, 'Type','patch');
+set(h(1), 'FaceColor',[.2,.2,.2], 'EdgeColor','w', 'linewidth',2)
+grid('off')
+h = gridxy([],get(gca,'ytick'),'color','w','linewidth',2)
 box('off');
+uistack(h, 'top')
+xlabel('Data')
+ylabel('Count')
+set(gcf, 'PaperUnits', 'centimeters');
+set(gcf, 'PaperSize', [11.7 9.0]);
+set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);