Besides simulating a discontinuous axis you could also draw an inset plot which shows only a ("zoomed") part of the plot.
For more details on how the solution works, please have a look at the comments in the code.
(Please note that I have created a dummy function to show some data, because the CSV file was not available when writing this answer.)
% used PGFPlots v1.14
\documentclass[border=5pt]{standalone}
\usepackage{pgfplots}
\pgfplotsset{
% enlare the axis limits
% (as it was requested in your other question
% <http://tex.stackexchange.com/q/358199>)
enlargelimits=true,
grid=major,
% I use this so it easier to set the two plots in a good ratio
% (because then the labels don't count to the `width' and `height')
scale only axis,
% now list the options that are in common for both plots
table/col sep=comma,
%
% these options are only for the dummy data, since the CSV file was not
% available when writing this answer
domain=0:450,
samples=51,
}
% declare some layers and their order
% these are needed if you want to have a background (color) behind the whole
% inset plot (including the `ticklabels' etc.) and not only the background
% of the "box" of the inset plot.
% You want to do at least one of these to avoid that also in the inset plot
% the grid lines of the "main" plot are shown/visible
\pgfdeclarelayer{background}
\pgfdeclarelayer{foreground}
\pgfsetlayers{background,main,foreground}
\begin{document}
\begin{tikzpicture}
% on the "lowest" layer, draw the normal plot
\begin{pgfonlayer}{background}
\begin{axis}[
width=6cm,
height=8cm,
xmin=0,
xmax=450,
ymin=1,
ymax=240,
% % if you really want to "cut off" some data, you can do this with this
% % key
% restrict x to domain=1:1000,
]
% \addplot [mark=x] table [x=size, y=cluster] {sim-0.3-0.6.csv};
% just a dummy function to produce a plot
\addplot {250*exp(-x/10)};
% store a coordinate where the inset should be plotted at
\coordinate (inset) at (axis description cs:0.95,0.95);
\end{axis}
\end{pgfonlayer}
% the inset plot should be plotted on the "top" most layer
\begin{pgfonlayer}{foreground}
% this is the inset plot ...
\begin{axis}[
% ... which should be plotted at the stored coordinate ...
at={(inset)},
% ... with this `anchor'
anchor=north east,
% use this predefined style (it is predefined by PGFPlots itself)
small,
%
% now state the options which should be used for the inset plot
width=3cm,
height=4cm,
xmin=1,
xmax=50,
ymin=1,
ymax=240,
% use this key to fill the background of the axis only
axis background/.style={
fill=white,
},
% name this axis so it can later be used to fill the "background" of the
% whole plot including the labels
name=insetAxis,
]
% \addplot [mark=x] table [x=size, y=cluster] {sim-0.3-0.6.csv};
% again the dummy plot
\addplot {250*exp(-x/10)};
\end{axis}
\end{pgfonlayer}
% on the "medium" layer we draw the background of the whole inset plot
% including the labels
\begin{pgfonlayer}{main}
% (I fill it with a gray here, so one can see the difference to the
% `axis background' result in the inset plot itself)
\fill [black!10] ([shift={(-2pt,-2pt)}] insetAxis.outer south west)
rectangle ([shift={(+5pt,+5pt)}] insetAxis.outer north east);
\end{pgfonlayer}
\end{tikzpicture}
\end{document}
