Here's a slightly adapted version of my answer to Drawing different tikz shapes parameterized by data from a file. It draws the circles using a scatterplots. You can choose to draw only every n-th mark using the mark repeat
key, choosing which entry to start with using the mark phase
key.
\documentclass{article}
\usepackage{pgfplots, filecontents}
\begin{filecontents}{data.dat}
# x y r
1 1 1
3 2 0.5
6 3 0.4
4 1 0.8
5 4 0.3
6 2 1
\end{filecontents}
\makeatletter
\begin{document}
\begin{tikzpicture}
\begin{axis}[scatter,
scatter src=explicit,
axis equal,
only marks,
grid=both,
width=10cm,
xmin=0, xmax=8,
disabledatascaling,
scatter/@pre marker code/.code={% Transform the data units to paper units
\pgfkeys{/pgf/fpu=true}
\pgfmathparse{(\pgfplotspointmeta*
10^\pgfplots@data@scale@trafo@EXPONENT@x)*\pgfplots@x@veclength)}
\pgfmathfloattofixed{\pgfmathresult}%
\pgfkeys{/pgf/fpu=false}
\scope[mark size=\pgfmathresult]
}
]
\addplot [fill=yellow, mark repeat=2] file {data.dat};
\end{axis}
\end{tikzpicture}
\end{document}