As a followup of this question, i am coping with drawing certain markers. And the solution by John Kormylo works fine for the presented MWE in that question. Here, I would like to extend the plot by two further data items, namely
\documentclass{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}
\begin{filecontents}{pgfplots-plot-limits.dat}
X Y color
0 0 0
0.45 0 1
0.5 0 2
0.55 0 3
\end{filecontents}%
\def\axisdim{6cm}% adjustable size
\begin{document}
\begin{tikzpicture}
\clip (0,0) rectangle (\axisdim,\axisdim);
\pgfdeclareplotmark{thiscube}{\draw[ultra thin, fill] (rel axis cs: 0.23438,-0.5) -- (rel axis cs: 0.26562,-0.5) --
(rel axis cs:-0.23438,0.5) -- (rel axis cs: -0.26562,0.5);}
\begin{axis}[colormap/hot,width=\axisdim,height=\axisdim,scale only axis=true,
xmin=-0.5, xmax=0.5, ymin=-0.5, ymax=0.5,
axis equal,xtick=\empty, ytick=\empty,hide axis
]
\addplot+[scatter,scatter src=explicit,mark=thiscube,only marks]
table [x=X,y=Y,meta=color] {pgfplots-plot-limits.dat};
\pgfplotsextra{\draw[thick,blue] (axis cs:-0.5,-0.5) rectangle (axis cs:0.5,0.5);}
\end{axis}
\end{tikzpicture}
\end{document}
Resulting in the following image

Which looks as a good solution, the markers are of right size, the first one is in the center (x=0) the right two ones are X=0.45 and X=0.5.
However, above the last one, another one (with same distance to the second last) should be present, namely the X=0.55 one. It is not drawn because its origin lies outside the range specifiex by xmin,xmax,ymin,ymax though
the marker reaches into the range.
Enlarging the range would (sadly) increase the relatively defined markers, which i don't want to (whether the clip would still work, i haven't checked).
Is there a way to disable this restriction, such that pgfplots would draw markers outside of the specified range? Or is there another solution to get the last data point to be drawn? That would be nice.
0.6 0 3(which is strange I think). I would like to see all markers that interleave with the given rectangle to be shown. – Ronny Mar 16 '16 at 13:27