[Tex/LaTex] Same pgfplots within standalone for usage in elsarticle and revtex4-1

best practiceselsarticlepgfplotsrevtexstandalone

Suppose I have created a plot with pgfplots for a scientific paper.

However, for usual reasons the targeted journal is not certain. Possibly the plot has to be adjusted to match different journals (consider here revtex4-1 and elsarticle). This includes font type, font sizes, columnwidths/textwidths.

For instance, the values of the \columnwidth differ:

% \documentclass[preprint,5p,twocolumn,12pt]{elsarticle}
\the\columnwidth=252.0pt
% \documentclass[aps,final,pre,twocolumn,10pt]{revtex4-1}
\the\columnwidth=246.0pt

I have considered the package standalone:

plot.tex:

\documentclass[class=elsarticle,5p,twocolumn,12pt]{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=1.5}
\begin{document}
\begin{tikzpicture}
\begin{axis}[
width=\columnwidth,
title=Inv. cum. normal,
xlabel={$x$},
ylabel={$y$},
]
\addplot[blue] table {invcum.dat};
\end{axis}
\end{tikzpicture}
\end{document}

download invcum.dat

paper.tex:

\documentclass[preprint,5p,twocolumn,12pt]{elsarticle}
\usepackage{lipsum}
\usepackage{graphicx}
\begin{document}
\setlength{\parindent}{0ex}
\lipsum[1]\vspace*{2ex}
\begin{figure}
  \centering
  \includegraphics{plot}
  \caption{interesting results}
\end{figure}
\vspace*{2ex}\lipsum[2]
\end{document}

After the paper got rejected :(, the documentclass gets changed.

paper.tex

\documentclass[final,aps,pre,twocolumn,10pt]{revtex4-1}

plot.tex

\documentclass[class=revtex4-1,final,aps,pre,twocolumn,10pt]{standalone}

For some reason standalone fails to accept as class option revtex4-1.

What would be a good workflow to minimize the workload using pdflatex without using dvi-eps path. Quantities, which should be available to plotting, are font size, \columnwidth and \textwidth.

An answer with a gnuplot+standalone solution would be a good addition.

Best Answer

You can use \includestandalone from standalone package (requires -shell-escape).

plot.tex:

\documentclass{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=1.5}
\begin{document}
\begin{tikzpicture}
\begin{axis}[
width=\columnwidth,
title=Inv. cum. normal,
xlabel={$x$},
ylabel={$y$},
]
\addplot[blue] table {invcum.dat};
\end{axis}
\end{tikzpicture}
\end{document}

Then in elsarticle:

\documentclass[preprint,twocolumn,12pt]{elsarticle}
\usepackage{lipsum}
\usepackage{graphicx}
%\usepackage{pgfplots}
%\pgfplotsset{compat=1.5}
\usepackage[subpreambles=true]{standalone}
\begin{document}
\setlength{\parindent}{0ex}
\lipsum[1]\vspace*{2ex}
\begin{figure}
  \centering
  \includestandalone[mode=buildnew]{plot}
  %\includegraphics{plot}
  \caption{interesting results}
\end{figure}
\vspace*{2ex}\lipsum[2]
\end{document}

enter image description here

And in revtex4-1

\documentclass[final,aps,pre,twocolumn,10pt]{revtex4-1}
\usepackage{lipsum}
\usepackage{graphicx}
%\usepackage{pgfplots}
%\pgfplotsset{compat=1.5}
\usepackage[subpreambles=true]{standalone}
\begin{document}
\setlength{\parindent}{0ex}
\lipsum[1]\vspace*{2ex}
\begin{figure}
  \centering
  \includestandalone[mode=buildnew]{plot}
  %\includegraphics{plot}
  \caption{interesting results}
\end{figure}
\vspace*{2ex}\lipsum[2]
\end{document}

enter image description here

Now, for curiosity, try with a big font size and different font.

\documentclass[18pt]{scrartcl}
\usepackage{lipsum}
\usepackage{mathpazo}
\usepackage{graphicx}
%\usepackage{pgfplots}
%\pgfplotsset{compat=1.5}
\usepackage[subpreambles=true]{standalone}
\begin{document}
\setlength{\parindent}{0ex}
\lipsum[1]\vspace*{2ex}
\begin{figure}
  \centering
  \includestandalone[mode=buildnew]{plot}
  %\includegraphics{plot}
  \caption{interesting results}
\end{figure}
\vspace*{2ex}\lipsum[2]
\end{document}

enter image description here

Related Solutions

PGFPlots – How to Plot Two Time Series with Bounds Using PGFPlots

This happens because PGFPlots only uses one "stack" per axis: You're stacking the second confidence interval on top of the first. The easiest way to fix this is probably to use the approach described in "Is there an easy way of using line thickness as error indicator in a plot?": After plotting the first confidence interval, stack the upper bound on top again, using stack dir=minus. That way, the stack will be reset to zero, and you can draw the second confidence interval in the same fashion as the first:

\documentclass{standalone}
\usepackage{pgfplots, tikz}

\usepackage{pgfplotstable}

\pgfplotstableread{
temps   y_h y_h__inf    y_h__sup    y_f y_f__inf    y_f__sup    

1   0.237340    0.135170    0.339511    0.237653    0.135482    0.339823    
2   0.561320    0.422007    0.700633    0.165871    0.026558    0.305184    
3   0.694760    0.534205    0.855314    0.074856    -0.085698   0.235411    
4   0.728306    0.560179    0.896432    0.003361    -0.164765   0.171487    
5   0.711710    0.544944    0.878477    -0.044582   -0.211349   0.122184    
6   0.671241    0.511191    0.831291    -0.073347   -0.233397   0.086703    
7   0.621177    0.471219    0.771135    -0.088418   -0.238376   0.061540    
8   0.569354    0.431826    0.706882    -0.094382   -0.231910   0.043146    
9   0.519973    0.396571    0.643376    -0.094619   -0.218022   0.028783    
10  0.475121    0.366990    0.583251    -0.091467   -0.199598   0.016664    
}{\table}

\begin{document}
\begin{tikzpicture}

    \begin{axis}
    % y_h confidence interval
    \addplot [stack plots=y, fill=none, draw=none, forget plot]   table [x=temps, y=y_h__inf]   {\table} \closedcycle;
    \addplot [stack plots=y, fill=gray!50, opacity=0.4, draw opacity=0, area legend]   table [x=temps, y expr=\thisrow{y_h__sup}-\thisrow{y_h__inf}]   {\table} \closedcycle;
    % subtract the upper bound so our stack is back at zero
    \addplot [stack plots=y, stack dir=minus, forget plot, draw=none] table [x=temps, y=y_h__sup] {\table};

    % y_f confidence interval
    \addplot [stack plots=y, fill=none, draw=none, forget plot]   table [x=temps, y=y_f__inf]   {\table} \closedcycle;
    \addplot [stack plots=y, fill=gray!50, opacity=0.4, draw opacity=0, area legend]   table [x=temps, y expr=\thisrow{y_f__sup}-\thisrow{y_f__inf}]   {\table} \closedcycle;

    % the line plots (y_h and y_f)    
    \addplot [stack plots=false, very thick,smooth,blue]  table [x=temps, y=y_h]   {\table};
    \addplot [stack plots=false, very thick,smooth,blue]  table [x=temps, y=y_f]   {\table};
    \end{axis}

\end{tikzpicture}
\end{document}

[Tex/LaTex] how to obtain exactly same size standalone pgfplots

As mentioned @JohnKormylo, the exact same size of images you can obtain with group plot. Since this is inconvenient solution for you, there is not much other option as I mentioned in my comments. With declaring width and height of images, where you should care that they are narrower than text width you obtain almost the same their size. Another care should give to height and depth of xlabels and xticks as well that have the same position. Since the plots are similar (I suspect this, however I'm not sure if this is a case) this should not be big deal. If they differ, you can help yourself with use of vphantom{...} construct or with

\rule[depth]{width}{height}

where you select zero width and appropriate depth and height.

Another advice is to draw images in size in which they will appear in document. All scaling can introduce discrepancy in image size.

I do not know why you prefer to include images as pdf files. Package standalone allows to included their files directly. With this you escape borders as you use in your files. In such approach I generated figure below:

I do not see visible differences between size of this images. Code for above example is:

\documentclass[a4paper, twoside, 12pt]{report}
    \usepackage{standalone}
\usepackage[a4paper,showframe,width=150mm,top=25mm,bottom=25mm]{geometry}
\usepackage[utf8]{inputenc}
\usepackage{pgfplots}
\usepackage{fixltx2e}
\usepackage{siunitx}
\usepackage{subfig}
\usepackage{xcolor}
\usepackage[version=4]{mhchem}

\DeclareSIUnit{\molar}{M}
\pgfplotsset{compat=newest,
            width=7cm, height=6cm,
            xtick pos=left, ytick pos=left,
%            scaled x ticks=real:1e-6,
            xtick scale label code/.code={},
            ylabel={$\Delta$ Absorbance}
            }

    \begin{document}
    \pagestyle{empty}
\begin{figure}[h]
\centering
\subfloat[]{%
\input{test-image-1}
            }%end of 1st subfloat
\hfil%
\subfloat[]{%
\input{test images-2
            }%end of 2nd subfloat
    \caption{}
\end{figure}
    \end{document}

Test images were generated with following files:

\documentclass[12pt,
               border=1pt]{standalone}
\usepackage[utf8]{inputenc}
\usepackage{pgfplots}
\usepackage{fixltx2e}
\usepackage{siunitx}
\usepackage{subfig}
\usepackage{xcolor}
\usepackage[version=4]{mhchem}

\DeclareSIUnit{\molar}{M}
\pgfplotsset{compat=newest,
            width=7cm, height=6cm,
            xtick pos=left, ytick pos=left,
%            scaled x ticks=real:1e-6,
            xtick scale label code/.code={},
            ylabel={$\Delta$ Absorbance}
            }

    \begin{document}
\begin{tikzpicture}
\begin{axis}[
    xlabel={$[\text{L}_{\text{PYR}}]_0 /\si{\micro\molar}$}
            ]
\addplot coordinates {
(5, 5)
(1, 1)
                    };
\end{axis}
\end{tikzpicture}
    \end{document}

The file for the second image differ from the above only in

\addplot coordinates {
(5, 5)
(1, 1)
                    };

I do not test above example with including images as pdf files. It should give the same result. As you can observe I place images slightly differently (more simply) into figure as you do in your MWE.

Best Answer

Related Solutions

PGFPlots – How to Plot Two Time Series with Bounds Using PGFPlots

[Tex/LaTex] how to obtain exactly same size standalone pgfplots

Related Question