Automatically align 104 subplot in pgfplots

Question

Using Matlab2tikz I generated a file containing 104 subplots aligned in a very specific manner. I then inserted \pgfplotsset{yticklabel style={text width=2em,align=right},}, compiled and obtained the final PDF which was fine, except the subplots arrangement is still not satisfactory:

I am trying to organize better the subplots such that:

1. there will be the same vertically spacing,
2. Only two ylabels per subplot

Is there a possibility to do this, without having to modify every single addplot?

Update: Using the solution proposed from Stefan Pinnow, I noticed that the order is still wrong. This is because the generated *.tikz file started from the second subplot (from the left) in the bottom row and positioned following subplots relative to it. This of course made the resulting figure using groupplot completely wrong. Hence, I think i am obliged to stick to the axis environment, and play on the yticklabels to improve the spacing.

Any idea how to automatically fix three yticklabels per subplot?

Answer 1

1. I think the easiest (consistent) way to implement this is using the groupplots library (have a look at section 5.8 of the PGFPlots manual on page 428ff (in v1.13).
2. Since you haven't specified exactly what "two ylabels" you need, I suggest playing a bit with the keys max space between ticks and try min ticks. Other keys of interest could be ytick (in combination with ytick distance) or yticklabels from table. All of these keys could be given as optional arguments to the \nextgroupplot command directly or - in case they should be repeated themselves - as styles which you can define in the preamble.

Please find a really simple example for the groupplot environment below.

\documentclass[border=2mm]{standalone}
\usepackage{pgfplots}
    \usepgfplotslibrary{groupplots}
\begin{document}
    \begin{tikzpicture}
        \begin{groupplot}[
            tiny,
            /tikz/mark size=1.5pt,
            group style={
                group name=my plots,
                group size=2 by 2,
                horizontal sep=4mm,      % <-- default: 1cm
                vertical sep=2mm,        % <-- default: 1cm
                xticklabels at=edge bottom,
            },
            width=3cm,
            height=3cm,
        ]
        \nextgroupplot[group/empty plot]
        \nextgroupplot
            \addplot coordinates{(0,0) (1,2) (2,1)};
        \nextgroupplot
            \addplot coordinates{(0,0) (1,2) (2,1)};
        \nextgroupplot
            \addplot coordinates{(0,0) (1,2) (2,1)};
        \end{groupplot}
    \end{tikzpicture}
\end{document}