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