Example of dynamic figure generation from raw data files

              
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%\title{Example of dynamic figure generation from raw data files}  
% Author: Joseph Wright
% Source: http://pgfplots.net/tikz/examples/cyclic-voltammetry/
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% This is a 'standalone' plot, so uses the standalone class
\documentclass{standalone}
%%%<
\usepackage{verbatim}
%%%>
\begin{comment}
:Title: Cyclic voltammetry
:Tags: 2D;Styles;Tufte;Chemistry
:Author: Joseph Wright
:Slug: cyclic-voltammetry

Visualization of chemical experiment data with Tufte style axes.
\end{comment}
% Making plots, so load the pgfplots package of course!
\usepackage{pgfplots}

% A bit of font set-up: use Latin Modern and T1 encoding
\usepackage[T1]{fontenc}
\usepackage{lmodern}

% For typesetting units
\usepackage{siunitx}

% For chemical information
\usepackage{chemformula}

% Use the latest settings, so we don't get trapped with old bugs or
% limited features.
\pgfplotsset{compat = newest}

% A few changes to how legends look: this is done for all plots.
\pgfplotsset{
  every axis legend/.append style =
    {
      % Change the text alignment so the end of the text (rather than the
      % start) lines up.
      cells = { anchor = east },
      % The standard pgfplots settings use a box around legends:
      % I prefer without this.
      draw  = none
    }
}

% Create a style to allow control of the settings: this will allow
% several plots to share the same setting without copy-pasting
\pgfplotsset{
  cyclic voltammetry/.style =
    {
      % Using a cycle list just altering colour means that there are no
      % marks: that is normal for this sort of plot.
      cycle list name = color list , 
      % Ensure that the x-axis values always have the same number of 
      % decimal places, to avoid e.g. "1" but "1.2".
      every x tick label/.append style  =
        { 
          /pgf/number format/.cd ,
           precision = 1 , 
           fixed         ,
           zerofill
        },
      % The labels apply to all plots of this type.
      % Notice that in this case the zero is ferrocenium/ferrocene, but that
      % will depend on the experiment.
      xlabel = $E / \si{\volt} \textrm{ \emph{versus} } \ch{Fc+}/\ch{Fc}$,
      % The normalised y-axis has something of a nightmare label!
      ylabel =
        $
          ( i / \si{\micro\ampere} )
            / \sqrt{\nu / ( \si{\milli\volt\per\second} ) }
        $,
    },
}

% Not everyone likes the 'axis box' effect which is the pgfplots default.
% Here, we'll set up to use 'Tufte-like' settings: see
% https://www.tug.org/members/TUGboat/tb34-2/tb107dugge.pdf for more on
% this.
\makeatletter
\pgfplotsset{
  tufte axes/.style =
    {
      after end axis/.code =
        {
          \draw ({rel axis cs:0,0} -| {axis cs:\pgfplots@data@xmin,0})
            -- ({rel axis cs:0,0}  -| {axis cs:\pgfplots@data@xmax,0});
          \draw ({rel axis cs:0,0} |- {axis cs:0,\pgfplots@data@ymin})
            -- ({rel axis cs:0,0}  |-{axis cs:0,\pgfplots@data@ymax});
        },
      axis line style = {draw = none},
      tick align      = outside,
      tick pos        = left
    }
}
\makeatother

\begin{document}
\begin{tikzpicture}
  \begin{axis}%
    [
      % Choose the general settings
      cyclic voltammetry,
      % and the Tufte style
      tufte axes,
      % Place the legend 'out of the way': this needs a bit of
      % experimentation!
      every axis legend/.append style = {at = {(0.9,0.5)}}
    ]
    % Loop for each scan rate
    \foreach \datafile in {50,500}
      {
        % For each case, add a plot
        \addplot
          table
            [
              % This plot extracts data directly from the instrument files.
              % To do that, we skip the first couple of lines.
              skip first n = 2 ,
              % The x-axis has a correction for the zero: that is done using
              % a simple expression
              x expr       = \thisrowno{0} + 0.412,
              % The y-axis is more complicated! There is a scaling so the
              % currents are in microamperes, and also a division by the
              % scan rate. The data files themselves are named using the
              % scan rate in millivolts per second: that is converted to 
              % volts per second before doing the square root.
              y expr       = 
                ( 1000000 * \thisrowno{1} )
                  / sqrt ( \datafile  / 1000 )
            ]
          from {\datafile.ocw}; 
        % Add a legend entry: the \datafile has to be forced to expand!  
        \addlegendentryexpanded{\SI{\datafile}{\milli\volt\per\second}};
      };  
  \end{axis}
\end{tikzpicture}
\end{document}