annotate-equations.tex

\documentclass{article}
\usepackage[a4paper, margin=1in]{geometry}

\usepackage[dvipsnames]{xcolor}

%%% standard math packages for equations:
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{mathtools}

\usepackage{hyperref}
\usepackage{cleveref}

\usepackage{annotate-equations}

%\usepackage{showexpl} % LTXexample
\usepackage[skins,listings]{tcolorbox}
\newtcblisting{LTXexample}[1][]{%
  colframe=black!20,
  colback=black!10,
  coltitle=red!50!yellow!3!white,
  bicolor,colbacklower=white,
  fonttitle=\sffamily\bfseries,
%  listing options={escapeinside=\`\`},
  %sidebyside,
  text above listing,
  #1}

\title{\texttt{annotate-equations.sty}, v.0.2.2}
\author{ST John}
\date{\url{https://github.com/st--/annotate-equations}}


\begin{document}

\maketitle



%\section{Introduction}

This package is there to make it easier to make annotated equations in \LaTeX, such as in this example:
\begin{LTXexample}[]
\vspace{4em}
\renewcommand{\eqnhighlightheight}{\vphantom{\hat{H}}\mathstrut}
\begin{equation*}
    i \tikzmarknode{hbar}{\mathstrut\hbar} \frac{\partial}{\partial t} \eqnmarkbox[blue]{Psi1}{\Psi(x, t)} = \eqnmark[red]{Hhat}{\hat{H}} \eqnmarkbox[blue]{Psi2}{\Psi(x, t)}
\end{equation*}
\annotate[yshift=3em]{above}{hbar}{$\hbar = \frac{h}{2\pi}$, reduced Planck constant}
\annotate[yshift=1em]{above}{Hhat}{Hamilton operator}
\annotatetwo[yshift=-1em]{below}{Psi1}{Psi2}{Wave function}
\vspace{1em}
\end{LTXexample}
There is still a bit of manual tweaking required (such as adding vertical space before/after the equation), but hopefully this package will already make it a bit more inviting to annotate your equations!

Note that this package relies on TikZ's \texttt{remember picture} option and therefore you have to compile your \LaTeX{} document at least twice to get everything in the right place (or just use \texttt{latexmk}!).


\tableofcontents


\section{Marking annotation targets within your equation}

\newcommand{\cmdoption}[1]{$\langle$\textit{#1}$\rangle$}

Use
\verb|\eqnmarkbox[|\cmdoption{color}\verb|]{|\cmdoption{node name}\verb|}{|\cmdoption{equation term(s)}\verb|}|
or
\verb|\eqnmark[|\cmdoption{color}\verb|]{|\cmdoption{node name}\verb|}{| \cmdoption{equation term(s)}\verb|}|
to define the target of an annotation within your equation. \verb|\eqnmarkbox| adds background shading, whereas \verb|\eqnmark| changes the text color.
(You can also use
\verb|\tikzmarknode{|\cmdoption{node name}\verb|}{|\cmdoption{equation term(s)}\verb|}|,
but this is likely to end up with the arrow tip too close to the target, so you may want to also pass the \texttt{outer ysep} option, see \cref{sec:outerysep}.)
%
\begin{LTXexample}[text outside listing,lefthand width=1in]
\begin{equation*}
    \eqnmarkbox[blue]{node1}{e_q^n}
    \eqnmark[red]{node2}{f(x)}
    \tikzmarknode{node3}{kT}
\end{equation*}
\end{LTXexample}
\noindent


\section{Simple annotations}
\label{sec:annotate}

Once you have defined nodes within your equations, you can annotate them using
\verb|\annotate[|\cmdoption{tikz options}\verb|]{|\cmdoption{annotate keys}\verb|}{|\cmdoption{node name[,\dots]}\verb|}{|\cmdoption{annotation text}\verb|}|.
%
\cmdoption{tikz options} is passed through to the options for the TikZ node defining the annotation; its most important use is to set the \texttt{yshift}.
For \cmdoption{annotate keys}, see \cref{sec:annotate-keys}.
\cmdoption{node name} is the same name you used to mark the node within the equation, e.g.\ using \verb|\eqnmarkbox|.
\cmdoption{annotation text} is the text of the annotation itself.
%
\begin{LTXexample}[text outside listing,lefthand width=1in]
\begin{equation*}
    \eqnmarkbox[blue]{node1}{e_q^n}
    \eqnmark[red]{node2}{f(x)}
    \tikzmarknode{node3}{kT}
\end{equation*}
\annotate[yshift=1em]{}{node1,node2}{my annotation text}
\end{LTXexample}
\noindent
%
\label{sec:tikz-options}
You generally need to manually adjust the \texttt{yshift} to move the annotations to an appropriate distance above (or negative values for below) the equation. If you want an annotation below the equation, with negative \texttt{yshift}, remember to also pass the \texttt{below} option (see \cref{sec:annotate-keys}).
(You can also adjust \texttt{xshift} if needed, also positive or negative.)

The annotation picks the same text color as given to \verb|\eqnmarkbox| or \verb|\eqnmark|, but you can also override it using \texttt{color} option.

One annotation can point to multiple targets, and multiple annotations can point to the same target.

\subsection{Annotation options}
\label{sec:annotate-keys}

\cmdoption{annotate keys} can be empty, or contain one or more of:
\begin{itemize}
    \item \texttt{above} (default) or \texttt{below},
    \item \texttt{right} (default) or \texttt{left},
    \item \texttt{label above} (default) or \texttt{label below}.

        Note: currently only works for \verb|\annotatetwo| (\cref{sec:annotatetwo}).
\end{itemize}
%
\begin{LTXexample}[text outside listing,lefthand width=1in]
\begin{equation*}
    \eqnmarkbox[blue]{node1}{e_q^n}
    \eqnmark[red]{node2}{f(x)}
    \tikzmarknode{node3}{kT}
\end{equation*}
\annotate[yshift=1em]{left}{node1}{my}
\annotate[yshift=-0.5em]{below,left}{node2}{annotation}
\annotate[yshift=-1em]{below, label below}{node3}{text}
\end{LTXexample}
\noindent
%


\section{Double annotations}
\label{sec:annotatetwo}

\verb|\annotatetwo[|\cmdoption{tikz options}\verb|]{|\cmdoption{annotate keys}\verb|}{|\cmdoption{first node name}\verb|}{|\cmdoption{second node name}\verb|}{|\cmdoption{annotation text}\verb|}|.
\cmdoption{tikz options} and \cmdoption{annotate keys} are as described above in \cref{sec:tikz-options,sec:annotate-keys}. Note that \cmdoption{annotate keys} \texttt{left}/\texttt{right} have no effect in \verb|\annotatetwo|.

\begin{LTXexample}[text outside listing,lefthand width=1in]
\begin{equation*}
    \eqnmarkbox[red]{a1}{a} \eqnmarkbox[blue]{b1}{b} = \eqnmarkbox[green]{b2}{b} \eqnmarkbox{a2}{a}
\end{equation*}
\annotatetwo[yshift=1.5em]{above, label below}{a1}{a2}{var 1}
\annotatetwo[yshift=0.5em]{above}{b1}{b2}{var 2}
\annotatetwo[yshift=-0.5em]{below}{b2}{b1}{var 2}
\end{LTXexample}
\noindent
%
Color is picked from the first of the two nodes.


\section{Package options}

\subsection{Size of highlight: shrink to content or always full height}

\verb|\eqnhighlightheight| is inserted into every \verb|\eqnhighlight|, \verb|\eqncolor|, \verb|\eqnmark|, and \verb|\eqnmarkbox| and by redefining it you can specify the minimum height for the corresponding box:
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnhighlightheight}{}  % package default

\begin{equation*}
    \eqnmarkbox[red]{hbar}{\hbar} \eqnmarkbox[blue]{q}{q}
\end{equation*}
\end{LTXexample}
\noindent
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnhighlightheight}{\mathstrut}  % 0-width "constant" height

\begin{equation*}
    \eqnmarkbox[red]{hbar}{\hbar} \eqnmarkbox[blue]{q}{q}
\end{equation*}
\end{LTXexample}
\noindent
%
\verb|\eqnhighlightheight| is used in math mode.


Note that in some cases \verb|\mathstrut| might not be enough, as in the introductory example:
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnhighlightheight}{\mathstrut}  % 0-width "constant" height

\begin{equation*}
    \eqnmarkbox[red]{Hhat}{\hat{H}} \eqnmarkbox[blue]{Psi}{\Psi}
\end{equation*}
\end{LTXexample}
\noindent
%
You can create custom 0-width characters using \verb|\vphantom|:
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnhighlightheight}{\vphantom{\hat{H}}\mathstrut}  % custom 0-width height

\begin{equation*}
    \eqnmarkbox[red]{Hhat}{\hat{H}} \eqnmarkbox[blue]{Psi}{\Psi}
\end{equation*}
\end{LTXexample}
\noindent
%
(It looks more balanced if you still include the \verb|\mathstrut|.)

\subsection{Amount of shading of mark highlight}

\verb|\eqnhighlightshade| defines the percentage of the specified color to take:
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnhighlightshade}{17}  % package default

\begin{equation*}
    \eqnmarkbox[red]{hbar}{\hbar} \eqnmarkbox[blue]{q}{q}
\end{equation*}
\end{LTXexample}
\noindent
%
By redefining this command, you can change the ``alpha'' value of the highlight:
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnhighlightshade}{47}  % 0 is white, 100 is solid color

\begin{equation*}
    \eqnmarkbox[red]{hbar}{\hbar} \eqnmarkbox[blue]{q}{q}
\end{equation*}
\end{LTXexample}
\noindent

\subsection{Default formatting of annotation labels}
\label{sec:eqnannotationfont}

\verb|\eqnannotationfont| sets the \texttt{font} field of the TikZ annotation label and can be re-set to change its formatting:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnannotationfont}{\sffamily\footnotesize}  % package default

\begin{equation*}
    \eqnmarkbox[blue]{v}{v}
\end{equation*}
\annotate[yshift=-0.5em]{below}{v}{velocity}
\vspace{1em}
\end{LTXexample}
\noindent
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnannotationfont}{\bfseries\small}

\begin{equation*}
    \eqnmarkbox[blue]{v}{v}
\end{equation*}
\annotate[yshift=-0.5em]{below}{v}{velocity}
\vspace{1em}
\end{LTXexample}
\noindent
%
Alternatively, you can also change the style of \verb|annotate equations/text|:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\tikzset{annotate equations/text/.style={font=\bfseries\small}}

\begin{equation*}
    \eqnmarkbox[blue]{v}{v}
\end{equation*}
\annotate[yshift=-0.5em]{below}{v}{velocity}
\vspace{1em}
\end{LTXexample}
\noindent

\verb|\eqnannotationstrut| is defined to be a strut (zero-width height) to
provide minimum distance between the text and the corresponding arrow line. By
default it is \verb|\strut|, which has a similar effect to
\verb|\mathstrut| in \verb|\eqnhighlightheight|.

\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnannotationstrut}{\strut}  % package default

\begin{equation*}
	\eqnmarkbox[blue]{size}{s}
\end{equation*}
\annotate[yshift=-0.5em]{below}{size}{The size}
\vspace{1em}
\end{LTXexample}
\noindent
%
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\renewcommand{\eqnannotationstrut}{}

\begin{equation*}
  \eqnmarkbox[blue]{size}{s}
\end{equation*}
\annotate[yshift=-0.5em]{below}{size}{The size}
\vspace{1em}
\end{LTXexample}


\subsection{Customize style}

You can change the style of the annotation arrow line by setting the style of \verb|annotate equations/arrow|:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\tikzset{annotate equations/arrow/.style={color=ForestGreen, >=latex', very thick, dashed}}

\begin{equation*}
  \eqnmarkbox[blue]{size}{s} = \eqnmarkbox[red]{other}{x}
\end{equation*}
\annotate[yshift=-0.5em]{below}{size}{The size}
\annotatetwo[yshift=1em]{above}{size}{other}{the same}
\end{LTXexample}
\noindent
Note that it applies to all \verb|\annotate| and \verb|\annotatetwo| arrows within the scope.

You can also use this to change the arrow direction:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\begin{equation*}
  \eqnmarkbox[blue]{size}{s} = \eqnmarkbox[red]{other}{x}
\end{equation*}
\tikzset{annotate equations/arrow/.style={->}}
\annotatetwo[yshift=1em]{above}{size}{other}{one and}
\tikzset{annotate equations/arrow/.style={<-}}
\annotatetwo[yshift=-1em]{below, label below}{size}{other}{the same}  % note that the "direction" of the arrow is from first to second mark
\end{LTXexample}

\section{Recommendations, tips \& tricks}

\subsection{Use \texttt{\textbackslash{}colorlet} for consistent, easily changeable colors}


\subsection{Mathematical relations such as ``$=$''}
\label{sec:mathrel}

Wrapping a mathematical relation symbol such as {\color{blue}$=$} in, for example, \texttt{\textbackslash{}tikzmarknode}, breaks how \TeX{} determines spacing in equations:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\[
a \tikzmarknode{node1}{=} b
\]
\annotate[yshift=-1em]{below}{node1}{equality}
\end{LTXexample}
\noindent
This can be fixed by wrapping the \texttt{\textbackslash{}tikzmarknode} in \texttt{\textbackslash{}mathrel}:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\[
a \mathrel{\tikzmarknode{node1}{=}} b
\]
\annotate[yshift=-1em]{below}{node1}{equality}
\end{LTXexample}

\subsection{Extra spacing between \texttt{\textbackslash{}tikzmarknode} and arrow}
\label{sec:outerysep}

If you want more space between arrow tip and annotated term, you can pass the \texttt{outer ysep} option to \texttt{\textbackslash{}tikzmarknode}:
\begin{LTXexample}[text outside listing,lefthand width=0.5in]
\[
a \mathrel{\tikzmarknode[outer ysep=5pt]{node1}{=}} b
\]
\annotate[yshift=-1em]{below}{node1}{equality}
\end{LTXexample}



\section{Known issues}

\begin{itemize}
    \item Annotations of mathematical relations require some manual patching to get the correct surrounding spacing (see \cref{sec:mathrel}).

\end{itemize}


\section{Backwards-incompatible changes}

\subsection*{v0.2.0}

\subsubsection*{\texttt{\textbackslash{}eqnannotationtext} removed}

To make it easier to format multiline annotations, version 0.2.0 introduced the \verb|\eqnannotationfont| and \verb|\eqnannotationstrut| (zero-argument) commands (see \cref{sec:eqnannotationfont}).

In exchange, the \verb|\eqnannotationtext| (one-argument) command was removed. To upgrade, replace for example
\begin{tcblisting}{listing only}
    \renewcommand{\eqnannotationtext}[1]{\sffamily\tiny#1\strut}
\end{tcblisting}
with
\begin{tcblisting}{listing only}
    \renewcommand{\eqnannotationfont}{\sffamily\tiny}
    \renewcommand{\eqnannotationstrut}{\strut}
\end{tcblisting}


\section{Examples}

The following examples are based on responses to GitHub issues: if you have any other requests for how to annotate questions, feel free to open an issue yourself on \url{https://github.com/st--/annotate-equations/issues}.

\subsection{Annotating a variable in multiple equations simultaneously}

\textit{For discussion, see \href{https://github.com/st--/annotate-equations/issues/25}{GitHub issue \#25}.}
\vspace{1em}

With two separate \verb|equation| environments:
\begin{LTXexample}[text outside listing,lefthand width=1.5in]
\begin{equation}
    b \eqnmarkbox[blue]{a1}{a} = c d
\end{equation}
\vspace{1.5em}  % make some space for annotation
\begin{equation}
    \eqnmarkbox[red]{a2}{a} e = f g
\end{equation}
\begin{tikzpicture}[overlay,remember picture]
    \coordinate (a2above) at (a2.north);
\end{tikzpicture}
\annotate[yshift=-0.4em]{below}{a1,a2above}{some variable}
\end{LTXexample}
Because \verb|\annotate| draws arrows from the north-anchors of the given nodes (for the \verb|{below}| option), we manually create an invisible point node at the correct place for the variables in the equation below the annotation.

It likewise works within a single \verb|align| environment:
\begin{LTXexample}[text outside listing,lefthand width=1.5in]
\begin{align}
    w \eqnmarkbox[blue]{b1}{b} &= c d \\[2.2em]  % make some space for annotation
    l \eqnmarkbox[red]{b2}{b} &= f g
\end{align}
\begin{tikzpicture}[overlay,remember picture]
    \coordinate (b2above) at (b2.north);
\end{tikzpicture}
\annotate[yshift=-0.2em]{below}{b1,b2above}{another variable}
\end{LTXexample}
In your own use-case, you may have to adjust the spacing and shifts as needed.

\vspace{1em}

{\it I am not sure if the \verb|[overlay,remember picture]| option to the \verb|tikzpicture| environment is actually needed; in these examples, it seems to work fine without, but if you encounter any problems, try to put it back. (And if you can confirm it will never be needed, please do re-open the GitHub issue and comment there to let me know!)}

\end{document}