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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}
