pgfplots: bar chart with scale "break" displays undesirable lines

Question

I'm trying to create a bar chart using pgfplots that has a scale "break" in the middle, to reasonably display both small bars and very large ones. Inspired by this answer, I got very close to my desired result using the following code:

\documentclass[a4paper,11pt]{article}

\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}

\usepackage{tikz}

\usetikzlibrary{patterns}

\usepackage{pgfplots}
\usetikzlibrary{pgfplots.groupplots}
\pgfplotsset{compat=1.16}

\begin{document}

\begin{figure}[p]
  \centering
  \begin{tikzpicture}
    \begin{groupplot}[
      width=\textwidth,
      height=19cm,
      symbolic x coords={brainfuck,queens,sha512,sha512Int},
      xtick=data,
      x tick label style={rotate=45,anchor=east},
      ytick distance=1,
      ymin=0, ymax=50,
      ymajorgrids=true,
      legend style={
        at={(0.5,-1.7cm)},
        anchor=north,
        legend columns=4,
      },
      ybar,
      group style={
        group size=1 by 2,
        xticklabels at=edge bottom,
        vertical sep=0pt,
      },
    ]

    \nextgroupplot[
      ymin=61,ymax=90,
      ytick distance=10,
      axis x line*=top,
      axis y discontinuity=parallel,
      height=4.5cm,
      bar width=7pt,
      enlarge x limits=0.15,
    ]
      \addplot[fill=lightgray] table [x=Benchmark,y=es5.1 dev no-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[fill=lightgray,postaction={pattern=north east lines}] table [x=Benchmark,y=es5.1 dev yes-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[] table [x=Benchmark,y=es5.1 prod no-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[pattern=north west lines] table [x=Benchmark,y=es5.1 prod no-opt yes-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[pattern=north east lines] table [x=Benchmark,y=es5.1 prod yes-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[pattern=crosshatch] table [x=Benchmark,y=es5.1 prod yes-opt yes-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};

    \nextgroupplot[
      ymin=0,ymax=20.5,
      ytick distance=3,
      axis x line*=bottom,
      height=14.5cm,
      bar width=7pt,
      enlarge x limits=0.15,
      ylabel=Normalized running time (lower is better),
    ]
      \addlegendimage{fill=lightgray}
      \addlegendentry{Dev mode}
      \addlegendimage{fill=white}
      \addlegendentry{Prod mode}
      \addlegendimage{pattern=north east lines}
      \addlegendentry{with Scala.js optimizer}
      \addlegendimage{pattern=north west lines}
      \addlegendentry{with GCC}

      \addplot[fill=lightgray] table [x=Benchmark,y=es5.1 dev no-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[fill=lightgray,postaction={pattern=north east lines}] table [x=Benchmark,y=es5.1 dev yes-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[] table [x=Benchmark,y=es5.1 prod no-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[pattern=north west lines] table [x=Benchmark,y=es5.1 prod no-opt yes-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[pattern=north east lines] table [x=Benchmark,y=es5.1 prod yes-opt no-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
      \addplot[pattern=crosshatch] table [x=Benchmark,y=es5.1 prod yes-opt yes-gcc Node.js,col sep=comma] {final-performance-results-slow-ones.csv};
    \end{groupplot}
  \end{tikzpicture}
  \caption{The effects of several optimization options on Node.js (part 2: the slow ones)}
  \label{fig:opts-options-on-nodejs-slow-ones}
\end{figure}

\end{document}

and the accompanying final-performance-results-slow-ones.csv:

Benchmark,es2015 prod yes-opt no-gcc Chrome,es2015 prod yes-opt no-gcc Firefox,es2015 prod yes-opt no-gcc Node.js,es5.1 dev no-opt no-gcc Chrome,es5.1 dev no-opt no-gcc Firefox,es5.1 dev no-opt no-gcc Node.js,es5.1 dev yes-opt no-gcc Chrome,es5.1 dev yes-opt no-gcc Firefox,es5.1 dev yes-opt no-gcc Node.js,es5.1 prod no-opt no-gcc Chrome,es5.1 prod no-opt no-gcc Firefox,es5.1 prod no-opt no-gcc Node.js,es5.1 prod no-opt yes-gcc Chrome,es5.1 prod no-opt yes-gcc Firefox,es5.1 prod no-opt yes-gcc Node.js,es5.1 prod yes-opt no-gcc Chrome,es5.1 prod yes-opt no-gcc Firefox,es5.1 prod yes-opt no-gcc Node.js,es5.1 prod yes-opt yes-gcc Chrome,es5.1 prod yes-opt yes-gcc Firefox,es5.1 prod yes-opt yes-gcc Node.js
brainfuck,3.86,7.69,3.46,9.27,17.79,8.92,6.08,7.08,5.73,6.65,15.21,6.31,6.24,11.17,5.99,3.80,4.93,3.41,3.42,4.22,3.26
queens,14.06,24.95,18.30,13.72,33.58,14.10,3.94,16.42,4.38,12.63,31.42,13.54,11.36,26.33,11.17,3.76,16.87,3.92,3.78,15.39,3.94
sha512,11.08,159.16,10.27,91.23,102.92,87.97,16.59,17.77,15.64,74.94,99.72,69.34,81.23,87.01,75.85,11.29,15.68,10.02,11.06,11.44,10.23
sha512Int,4.83,8.45,4.14,19.98,13.16,18.88,9.36,10.72,8.56,12.15,11.80,11.48,10.47,9.73,10.00,4.54,3.50,4.01,4.59,3.30,4.04

This renders my graph almost exactly as I would like, except that there are undesirable small horizontal lines at the level of the break, one for each bar:

Obviously, I'd like those horizontal bars not to be there. How could I get rid of them?

The version of pgfplots I have is 1.16. I use PDFLaTeX.

Answer 1

The "horizontal lines" are caused by the bars that should not be present in the upper part of the plot. You can remove them by adding a y filter. Then, the only remaining "horizontal lines" are the ones in the bars that are shown in the upper plot.

Unfortunately I think, staying with this solution it will be really hard to get rid of these lines ...

For more details, please have a look at the comments in the code.

% used PGFPlots v1.16
\documentclass[border=5pt]{standalone}
\usepackage{tikz}
    \usetikzlibrary{patterns}
\usepackage{pgfplots}
    \usetikzlibrary{pgfplots.groupplots}
    \pgfplotsset{compat=1.16}
\begin{document}
  \begin{tikzpicture}
    \begin{groupplot}[
      width=\textwidth,
      height=19cm,
      % -----------------------------------------------------------------------
%      % replaced this ...
%      symbolic x coords={brainfuck,queens,sha512,sha512Int},
      % ... by these two lines
      xtick=data,
      xticklabels from table={final-performance-results-slow-ones.csv}{Benchmark},
      % -----------------------------------------------------------------------
      x tick label style={rotate=45,anchor=east},
      ytick distance=1,
      ymin=0, ymax=50,
      ymajorgrids=true,
      legend style={
        at={(0.5,-1.7cm)},
        anchor=north,
        legend columns=4,
      },
      ybar,
      group style={
        group size=1 by 2,
        xticklabels at=edge bottom,
        vertical sep=0pt,
      },
      % -----------------------------------------------------------------------
      % (moved common options here)
      /tikz/bar width=7pt,
      enlarge x limits=0.15,
      table/col sep=comma,
      cycle list={
        {fill=lightgray},
        {fill=lightgray,postaction={pattern=north east lines}},
        {},
        {pattern=north west lines},
        {pattern=north east lines},
        {pattern=crosshatch},
      },
      % -----------------------------------------------------------------------
%      % replaced this ...
%      table/x=Benchmark,
      % by this to match the replaced `symbolic x coords' line
      table/x expr=\coordindex,
      % -----------------------------------------------------------------------
    ]

    \nextgroupplot[
      ymin=61,ymax=90,
      ytick distance=10,
      axis x line*=top,
      axis y discontinuity=parallel,
      height=4.5cm,
      %
      xmin=0,
      xmax=3,
      % -----------------------------------------------------------------------
      % filter away the "horizontal lines"
      y filter/.code={
        \pgfmathifthenelse{#1 < 61}{NaN}{#1},
      },
      % -----------------------------------------------------------------------
    ]
      \addplot table [y=es5.1 dev no-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 dev yes-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod no-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod no-opt yes-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod yes-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod yes-opt yes-gcc Node.js] {final-performance-results-slow-ones.csv};

    \nextgroupplot[
      ymin=0,ymax=20.5,
      ytick distance=3,
      axis x line*=bottom,
      height=14.5cm,
      ylabel=Normalized running time (lower is better),
    ]
      \addlegendimage{fill=lightgray}
      \addlegendentry{Dev mode}
      \addlegendimage{fill=white}
      \addlegendentry{Prod mode}
      \addlegendimage{pattern=north east lines}
      \addlegendentry{with Scala.js optimizer}
      \addlegendimage{pattern=north west lines}
      \addlegendentry{with GCC}

      \addplot table [y=es5.1 dev no-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 dev yes-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod no-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod no-opt yes-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod yes-opt no-gcc Node.js] {final-performance-results-slow-ones.csv};
      \addplot table [y=es5.1 prod yes-opt yes-gcc Node.js] {final-performance-results-slow-ones.csv};

    \end{groupplot}
  \end{tikzpicture}
\end{document}