mass_spectrum.tex

% Defines a macro for showing mass spectra
\usepackage{options}
\usepackage{environ}
\usepackage{pgfmath}
\usepackage{pgfplotstable}

\options{
    /MassSpectrum/.new family,
    /MassSpectrum/dim/width/.new length         = 0.9\textwidth,
    /MassSpectrum/dim/height/.new length        = 8cm,
    /MassSpectrum/mz/min/.new value             = 40,
    /MassSpectrum/mz/max/.new value             = 250,
    /MassSpectrum/caliper/yoffset/.new value    = 2,
}

\NewEnviron{MassSpectrumEnvironment}[1]{
    {\options{/MassSpectrum,#1}{
    \BODY
    }}
}

\newcommand{\MassSpectrum}[2]{

    \pgfplotstableread[col sep=comma]{#1}{\data}
    \MassSpectrumIndexIntensities{\data}
    
    \begin{tikzpicture}
    
    \begin{axis}[
        ycomb,mark=none,
        %==========================================
        ylabel={Relative Intensity (\si{\percent})},
        xlabel={Mass-to-Charge Ratio ($m/z$)},
        %==========================================
        xmin=\option{/MassSpectrum/mz/min},
        xmax=\option{/MassSpectrum/mz/max},
        %==========================================
        width=\option{/MassSpectrum/dim/width},
        height=\option{/MassSpectrum/dim/height},
        %==========================================
        ymin=0,ymax=110,
        xtick pos=left,
        xtick align=outside,
        ytick pos=left,
        ytick align=outside,
    ]
%
    \addplot[
        no markers
    ] table[x=mass,y=intensity] {\data};
%
    #2
%
    \end{axis}

    \MassSpectrumIndexInstensitiesClear{\data}
    \end{tikzpicture}
}

\newcommand{\MassSpectrumIndexIntensities}[1]{
    \pgfplotstableforeachcolumnelement{mass}\of{#1}\as\mass{%
        \pgfplotstablegetelem{\pgfplotstablerow}{intensity}\of{#1}
        \expandafter\pgfmathsetmacro\csname massSpec\mass\endcsname{\pgfplotsretval}
    }
}

\newcommand{\MassSpectrumIndexInstensitiesClear}[1]{
    \pgfplotstableforeachcolumnelement{mass}\of{#1}\as\mass{%
        \expandafter\pgfmathsetmacro\csname massSpec\mass\endcsname{}
    }
}

\newcommand{\MassSpectrumGetIntensityAt}[1]{
    \expandafter{\csname massSpec#1\endcsname}
}

\newcommand{\MassSpectrumTitle}[1]{
    \node[anchor=north west] at (rel axis cs:0,1) {#1};
}

\newcommand{\MassSpectrumWriteText}[3]{
    \node[anchor=south] at (axis cs: #1, #2) {\footnotesize{#3}};
}

\newcommand{\MassSpectrumCalloutManual}[2]{
    \MassSpectrumWriteText{#1}{#2}{#1}
}

\newcommand{\MassSpectrumCallout}[1]{
    \MassSpectrumCalloutManual{#1}{\MassSpectrumGetIntensityAt{#1}}
}

\newcommand{\MassSpectrumCalloutAnnotate}[4]{
    \draw[help lines]
         (axis cs:#3,#4)
      -- (axis cs:#1,#2);
    \node[style={fill=white}] at (axis cs:#3,#4) {\footnotesize{#1}} -- (axis cs:#1,#2);
}


\newcommand{\MassSpectrumCaliper}[4]{
    \draw[help lines, |-]
         (axis cs:#1,\MassSpectrumGetIntensityAt{#1}+\option{/MassSpectrum/caliper/yoffset})
      -- (axis cs:#1,#3);

    \draw[help lines, |-]
         (axis cs:#2,\MassSpectrumGetIntensityAt{#2}+\option{/MassSpectrum/caliper/yoffset})
      -- (axis cs:#2,#3);

    \draw[help lines]
         (axis cs:#1,#3)
      -- (axis cs:#2,#3)
    node [midway, centered, sloped, text=black, style={fill=white}] {\footnotesize{#4}};
}

\begin{figure}
    \centering

    \begin{MassSpectrumEnvironment}{
        mz/min=0,
        mz/max=90
    }
        \MassSpectrum{isobutelene_epoxide.csv}{
            \MassSpectrumTitle{Isobutelene epoxide}
            \MassSpectrumCallout{27}
            \MassSpectrumCalloutAnnotate{41}{95}{35}{90}
            \MassSpectrumCallout{72}

            \MassSpectrumCaliper{57}{43}{60}{-H\textsubscript{2}O}
        }
    \end{MassSpectrumEnvironment}
    \caption{Caption}
    \label{fig:enter-fdgdfgdfgdfjk}
\end{figure}