[plotting] object way of editing plot properties

plotting/code/annotations.m

@@ -1,10 +1,12 @@
 time = 0.0:0.001:1.0;
 y = sin(2 * pi * 2 .* time);
 
-figure
 hold on
-set(gcf, 'Color', 'white', 'PaperUnit', 'centimeters', 'PaperSize', [4 4], ... 
+fig = figure();
-    'PaperPosition', [0 0 4 4])
+fig.PaperUnits = 'centimeters';
+fig.PaperSize = [4 4];
+fig.PaperPosition = [0.0 0.0 4, 4];
+fig.Color = 'white';
 
 plot(time, y)
 plot([0.0 1.0], [0.0 0.0], '--', 'color','k', 'linewidth', 0.75)

plotting/code/automatic_plot.m

@@ -1,26 +1,40 @@
 load('pyramidal_response.mat')
 threshold = 20; % mV
 
-hold on
+hold on;
 plot(time*1000.0, neuronal_data, 'color', [0.2 0.5 0.7], ...
-    'linewidth', 1., 'displayname', 'Membrane voltage')
+     'linewidth', 1., 'displayname', 'Membrane voltage');
 plot(spikes*1000.0, ones(size(spikes)) .* threshold, 'r.', ...
-    'markersize', 15, 'displayname', 'Spike times')
+     'markersize', 15, 'displayname', 'Spike times');
 line([time(1) time(end)], [threshold threshold], 'linestyle', '--', ...
-    'linewidth', 0.75, 'color', [0.5 0.5 0.5], 'displayname', 'Threshold')
+     'linewidth', 0.75, 'color', [0.5 0.5 0.5], 'displayname', 'Threshold');
 
-xlabel('Time [ms]', 'fontname', 'times', 'fontsize', 11)
+axes = gca();
-ylabel('Potential [mV]', 'fontname', 'times', 'fontsize', 11)
+axes.XLabel = 'Time [ms]';
-title('ELL pyramidal neuron', 'fontname', 'times', 'fontsize', 12)
+axes.YLabel = 'Potential [mV]';
-ylim([0 40])
+axes.Title = 'ELL pyramidal neuron';
-xlim([500 1700])
+axes.XLim = [[500 1700];
-box('off')
+axes.YLim = [0 40];
-l = legend(gca,'show');
+axes.XMinorTick = 'on';
-set(l,'location','northeast', 'fontsize', 11, 'linewidth', 1.);
+axes.YMinorTick = 'on';
-set(gca, 'xminortick','on','yminortick','on')
+axes.TickDir = 'out';
-set(gca, 'tickdir','out', 'linewidth', 1.5, 'fontname', 'times', ...
+axes.LineWidth = 1.5;
-    'fontsize', 11)
+axes.box('off')
-set(gcf, 'paperunits', 'centimeters', 'papersize', [15 7]);
-set(gcf, 'paperposition',[0.0 0.0 15, 7], 'color', 'white')
 
-saveas(gcf, 'spike_detection.pdf', 'pdf')
+axes.FontName = 'Times';
+axes.FontSize = 8;
+axes.TitleFontSizeMultiplier = 1.5;
+axes.LabelFontSizeMultiplier = 1.25;
+
+l = legend(axes, 'show');
+l.Location = "northeast";
+l.FontSize = 11;
+l.LineWidth = 1;
+
+fig = gcf();
+fig.PaperUnits = 'centimeters';
+fig.PaperSize = [15, 7];
+fig.PaperPosition = [0.0 0.0 15, 7];
+fig.Color = 'white';
+
+saveas(gcf, 'spike_detection.pdf', 'pdf')

plotting/code/errorbarplot.m

@@ -11,8 +11,11 @@ err_upper_asym = prctile(asym_data, 75, 1);
 err_lower_asym = prctile(asym_data, 25, 1);
 
 fig = figure();
-set(fig, 'paperunits', 'centimeters', 'papersize', [15 6.5], ...
+fig.PaperUnits = 'centimeters';
-    'paperposition', [0.0 0.0 15, 6.5], 'color', 'white')
+fig.PaperSize = [15 6.5];
+fig.PaperPosition = [0.0 0.0 15, 6.5];
+fig.Color = 'white';
+
 subplot(1,3,1)
 errorbar(x_data, avg_sym, err_sym, 'marker', 'o')
 xlim([-.5, 6.5])

plotting/code/movie_example.m

@@ -7,9 +7,11 @@ f_y = 1.5;
 dt = 2*pi/500;
 
 f = figure();
-set(f, 'visible', 'off');
+f.Visible = false;
-set(f, 'PaperUnits', 'centimeter', 'PaperSize', [2.5, 2.5], ...
+f.PaperUnits = 'centimeters';
-    'PaperPosition', [0, 0, 2.5, 2.5], 'Color', 'white')
+f.PaperSize = [2.5 2.5];
+f.PaperPosition = [0.0 0.0 2.5, 2.5];
+f.Color = 'white';
 
 writer = VideoWriter('../lecture/images/lissajous.mp4', 'MPEG-4');
 writer.FrameRate = 25;
@@ -40,8 +42,10 @@ for i = 1:max_frames
 end
 
 f = figure();
-set(f, 'PaperUnits', 'centimeter', 'PaperSize', [5, 5], ...
+f.PaperUnits = 'centimeters';
-    'PaperPosition', [0, 0, 5, 5], 'Color', 'white')
+f.PaperSize = [2.5 2.5];
+f.PaperPosition = [0.0 0.0 2.5, 2.5];
+f.Color = 'white';
 
 scatter(x_positions, y_positions, 10, 'r', 'filled');
 xlim([-1.05, 1.05])
@@ -51,4 +55,4 @@ yticks([-1., 0., 1.])
 xlabel('x')
 ylabel('y')
 
-saveas(f, '../lecture/images/lissajous.png')
+saveas(f, '../lecture/images/lissajous.png')

plotting/code/simple_plot.m

@@ -1,5 +1,5 @@
 frequency = 5;          % frequency of the sine wave in Hz
-time = 0.01:0.01:1.0;   % the time axis
+time = 0.01:0.01:1.0;   % the time axis in seconds
 signal = sin(2 * pi * time * frequency);
 
 plot(time, signal);

plotting/lecture/plotting.tex

@@ -3,7 +3,7 @@
 We may count the ability of adequately presenting scientific data to
 the core competences needed to do science. We need to present data in
 a meaningful way that supports understanding of the data and the
-results.
+results without biases.
 
 \begin{figure}[hb!]
   \includegraphics[width=0.9\columnwidth]{convincing}
@@ -15,13 +15,13 @@ results.
 
 Plotting data in \matlab{} is rather straight forward for simple line
 plots. By calling \code[plot()]{plot(x, y)} a simple line plot will be
-created. This figure, however is missing any annotations like axis
+created. The resulting figure, however is missing any annotations like axis
 labeling, a legend, etc.. There are two options to edit the plot: (i)
 the graphical user interface (GUI) or the command line. Both ways have
 their right to exist associated with respective pros and cons. The UI
-way of editing plots is ideal for experimenting the command line
+way of editing plots is ideal for experimenting, the command line
 approach is best suited for automation and to achieve a consistent
-layout across figures and graphs.
+layout across figures and graphs in a paper or thesis.
 
 \begin{figure}
   \begin{minipage}[t]{0.6\textwidth}
@@ -95,31 +95,35 @@ number of datasets.
 Creating a simple line-plot is rather easy. Assuming there exists a
 variable \varcode{y} in the \codeterm{Workspace} that contains the
 measurement data it is enough to call \code[plot()]{plot(y)}. At the
-first call of this function a new window will be opened and the data
+first call of this function a new \codeterm{figure} will be opened and
-will be plotted with as a line plot. If you repeatedly call this
+the data will be plotted with as a line plot. If you repeatedly call
-function the current plot will be replaced unless the \code[hold]{hold
+this function the current plot will be replaced unless the
-  on} command was issued before. If it was, the current plot is held
+\code[hold]{hold on} command was issued before. If it was, the current
-and a second line will be added to it. Calling \code[hold]{hold off}
+plot is held and a second line will be added to it. Calling
-will release the plot and any subsequent plotting will replace the
+\code[hold]{hold off} will release the plot and any subsequent
-previous plot.
+plotting will replace the previous plot.
-
+
-In our previous call to \varcode{plot} we have provided just a single
+In our previous call to \varcode{plot} we provided just a single
 variable containing the y-values of the plot. The x-axis will be
 scaled from zero to the number of elements in \varcode{y} the x-values
 are automatically substituted assuming a constant stepsize of 1. This
 automatic scaling is probably not desired and thus, we need to provide
-the missing information ourselves. The respective call will expand to
+the missing information ourselves. Thus, we need a second variable
-\code[plot()]{plot(x, y)}. In axis will be scaled from the minimum in
+that contains the respective \varcode{x} values. The length of
-\varcode{x} to the maximum of \varcode{x} and by default it will be
+\varcode{x} and \varcode{y} must be the same otherwise the later call
-plotted as a line plot with a solid blue line of the with 1pt. A
+of the \varcode{plot} function will raise an error. The respective
-second plot that is added to the figure will be plotted in red using
+call will expand to \code[plot()]{plot(x, y)}. The x-axis will be now
-the same standard settings. The order of the used colors depends on
+be scaled from the minimum in \varcode{x} to the maximum of
-the \enterm{colormap} settings which can be adjusted to personal taste
+\varcode{x} and by default it will be plotted as a line plot with a
-or need. Table\,\ref{plotlinestyles} shows some predefined values that
+solid blue line of the linewidth 1pt. A second plot that is added to the
+figure will be plotted in red using the same settings. The
+order of the used colors depends on the \enterm{colormap} settings
+which can be adjusted to personal taste or
+need. Table\,\ref{plotlinestyles} shows some predefined values that
 can be chosen for the line style, the marker, or the color. For
 additional options consult the help.
 
-\begin{table}[tp]
+\begin{table}[htp]
   \titlecaption{Predefined line styles (left), colors (center) and
     marker symbols (right).}{}\label{plotlinestyles}
   \begin{tabular}[t]{lc} \hline
@@ -173,33 +177,29 @@ chosen.
     not distinguish between red and green.
   \item Can you distinguish the colors in a b/w respectively gray
     scale print?
-  \item Color figures in publications often cost extra money.
+  \item Color figures in publications sometimes cost extra money.
   \end{itemize}
 \end{important}
 
-\subsection{Changing the axis properties}
+\subsection{Changing the axes properties}
-
+
-The first thing a data plot needs are axis labels with a correct
+The first thing a plot needs are axis labels with correct units. By
-unit. By calling the functions \code[xlabel]{xlabel('Time [ms]')} and
+calling the functions \code[xlabel]{xlabel('Time [ms]')} and
-\code[ylabel]{ylabel{'Voltage [mV]'}} these can be set. By default the
+\code[ylabel]{ylabel('Voltage [mV]')} these can be set. By default the
-axes will be scaled to show the whole data range. The extremes will be
+axes will be scaled to show the full extent of the data. The extremes
-selected as the closest integer for small values or the next full
+will be selected as the closest integer for small values or the next
-multiple of tens, hundreds, thousands, etc.\ depending on the maximum
+full multiple of tens, hundreds, thousands, etc.\ depending on the
-value. If these defaults do not match our needs, the limits of the
+maximum value. If these defaults do not match your needs, the limits
-axes can be explicitly set with the functions \code[xlim()]{xlim()}
+of the axes can be explicitly set with the functions
-and \code[ylim()]{ylim()}. To do this, the functions expect a single
+\code[xlim()]{xlim()} and \code[ylim()]{ylim()}. To do this, the
-argument, that is a vector containing the minimum and maximum
+functions expect a single argument, that is a 2-element vector
-value. Table\,\ref{plotaxisprops} lists some of the commonly adjusted
+containing the minimum and maximum value. Table\,\ref{plotaxisprops}
-properties of an axis. These properties can be set using the
+lists some of the commonly adjusted properties of an axis. To set
-\code[set()]{set()} function. The \code{set} function expects as a
+these properties, we need to have the axes object which can either be
-first argument a \enterm{handle} of the affected axis. An axis handle
+stored in a variable when calling \varcode{plot} (\code{axes =
-of the current plot is returned by the \code[gca]{gca} function (gca
+  plot(x,y);}) or can be retrieved using the \code[gca]{gca} function
-stands for ``get current axis''). The following arguments passed to
+(gca stands for ``get current axes''). Changing the properties of the axes
-\code{set} are pairs of the property name and the desired value. It is
+object will update the plot (listing\,\ref{niceplotlisting}).
-possible to set any number of properties using a single call to
-\code{set}. See listing\,\ref{niceplotlisting} (lines 20 and 21) for
-an example (these commands could be joined into a single call to
-\code{set} but have been split for better readability).
 
 \begin{table}[tp] 
   \titlecaption{Incomplete list of axis properties.}{For a complete
@@ -247,27 +247,30 @@ an example (these commands could be joined into a single call to
   \end{tabular*}
 \end{table}
 
-Like axes, also figure has several properties that can be adjusted to
+Like the axes, also the figure has several properties that can be
-the current needs. Most notably the paper (figure) size and the
+adjusted to the current needs. Most notably the paper (figure) size
-placement of the axes on the paper. Table\,\ref{plotfigureprops} lists
+and the placement of the axes on the
-commonly used properties. For a complete reference check the help. To
+paper. Table\,\ref{plotfigureprops} lists commonly used
-change the properties, we again use the \code{set()} function. The
+properties. For a complete reference check the help. To change the
-first argument is now a handle to the current figure, not the current
+figure's appearance, we need to change the properties of the figure
-axis as before. Analogously to the \code{gca} command there is a
+object which can be retrieved during creation of the figure (\code{fig
-\code{gcf} (``get current figure'') command with which the handle can
+  = figure();}) or by using the \code{gcf} (``get current figure'')
-be retrieved.
+command.
 
 The script shown in the listing\,\ref{niceplotlisting} exemplifies
 several features of the plotting system and automatically generates
 and saves figure\,\ref{spikedetectionfig}. With any execution of this
 script exactly the same plot will be created. If we decided to plot a
 different recording, the format will stay exactly the same, just the
-data changes. Of special interest are the lines 22 and 23 which set
+data changes. Of special interest are the lines 35 through 37 which
-the size of the figure and positions the axes on the paper. Line 26
+set the size of the figure and positions the axes on the paper. Lines
-finally saves the figure in the 'pdf' format to file. When calling the
+24 through 27 control the font used for labeling inside the axes. The
-function \code{saveas()} the first argument is the current figure
+axes holds the default \varcode{FontSize} and via multipliers applied
-handle, the second the file name, and the last one defines the
+to the default one can control the size of the title (line 26) or the
-output format (box\,\ref{graphicsformatbox}).
+axes labels (line 27). Line 40 finally saves the figure in the 'pdf'
+format to file. When calling the function \code{saveas()} the first
+argument is the current figure handle, the second the file name, and
+the last one defines the output format (box\,\ref{graphicsformatbox}).
 
 \begin{figure}[t]
   \includegraphics{spike_detection} \titlecaption{Automatically
@@ -325,6 +328,37 @@ output format (box\,\ref{graphicsformatbox}).
   label=niceplotlisting]{automatic_plot.m}
 
 
+\begin{ibox}[t]{\label{handlevsobjectbox}The wind of change.}
+  The way figure or axis properties can be adapted has been changed
+  with recent \matlab{} versions. In versions before \emph{R2014b}
+  properties could be read and set using the functions
+  \code[get()]{get} and \code[set()]{set}. The first argument these
+  functions expect are valid figure or axis \emph{handles} which were
+  returned by the \code{figure} and \code{plot} functions, or could be
+  retrieved using \code[gcf()]{gcf} or \code[gca()]{gca} for the
+  current figure or axis handle, respectively. Subsequent arguments
+  passed to \code{set} are pairs of a property's name and the desired
+  value.
+  \begin{lstlisting}[caption={Using set to change figure and axis properties.}]
+    frequency = 5;          % frequency of the sine wave in Hz
+    time = 0.01:0.01:1.0;   % the time axis in seconds
+    signal = sin(2 * pi * time * frequency);
+    plot(time, signal)      
+
+    axes_handle = gca();     % get current axes
+    figure_handle = gcf();   % get current figure
+    set(axes_handle, 'XLabel', 'time [s]', 'YLabel', 'amplitude');
+    set(figure_handle, 'PaperSize', [5.5, 5.5], 'PaperUnit', 'centimeters', ...
+        'PaperPosition', [0, 0, 5.5, 5.5]);    
+  \end{lstlisting}
+  With newer versions the handles returned by \varcode{gcf} and
+  \varcode{gca} are ``objects'' and setting properties became much
+  easier as it is used throughout this chapter.  For downward
+  compatibility with older versions set and get still work in current
+  versions of \matlab{}.
+\end{ibox}
+
+
 \section{Plot examples}
 
 So far we have introduced the standard line plots. Next to these there
@@ -485,7 +519,7 @@ its properties. See the \matlab{} help for more information.
 
 \lstinputlisting[caption={Illustrating estimation errors using error bars. Script that
     creates \figref{errorbarplot}. A, B},
-  label=errorbarlisting, firstline=13, lastline=29,
+  label=errorbarlisting, firstline=13, lastline=31,
   basicstyle=\ttfamily\scriptsize]{errorbarplot.m}
 
 \subsubsection{Fill}
@@ -507,7 +541,7 @@ version of the x-values to the original x-values using \code{cat} and
 \code{fliplr} for concatenation and inversion, respectively (line 3 in
 listing \ref{errorbarlisting2}; Depending on the layout of your data
 you may need concatenate along a different dimension of the data and
-use \code{flipud} instead). The y-coordinates of the polygon vertices
+use \code{flipud} instead). The y-coordinates of the polygon vertices 
 are concatenated in a similar way (line 4). In the example shown here
 we accept the polygon object that is returned by fill (variable p) and
 use it to change a few properties of the polygon. The \emph{FaceAlpha}
@@ -519,7 +553,7 @@ connecting the average values (line 12).
 
 \lstinputlisting[caption={Illustrating estimation errors using a shaded area. Script that
     creates \figref{errorbarplot} C.}, label=errorbarlisting2,
-  firstline=30,
+  firstline=33,
   basicstyle=\ttfamily\scriptsize]{errorbarplot.m}
 
 \subsection{Annotations, text}
@@ -600,7 +634,7 @@ Lissajous figure. The basic steps are:
 \end{enumerate}
 
 \lstinputlisting[caption={Making animations and saving them as a
-    movie.}, label=animationlisting, firstline=3, lastline=33,
+    movie.}, label=animationlisting, firstline=16, lastline=36,
   basicstyle=\ttfamily\scriptsize]{movie_example.m}
 
 \section{What makes a good plot?}