pgfplots how to nicely place nodes

Question

The picture produced by code blow, there are two problems I have.

(1) the number above point overlapped

(2) the precision of number is not right, eg. I want 0.913, not 0.91

For the first problem I tried the 'nodes near coords align', but no good result. Is there a way to solve this?

\documentclass[12pt]{article}
\usepackage{tikz}
\usepackage{pgfplots}
\usepackage{filecontents}
\pagestyle{empty}

\begin{filecontents}{x.dat}
1,0.304313797
2,0.558012673
3,0.741302281
4,0.851281192
5,0.912940189
6,0.945961019
7,0.964838045
8,0.975736752
9,0.982694892
\end{filecontents}

\begin{document}
    \begin{tikzpicture}
        \begin{axis}[
            axis x line=bottom,
            axis y line=left,
            xlabel={Query Length},
            ylabel={Percentage},
            xmin=0,
            ymin=0,
            xmax=10,
            ymax=1,
            xtick={0,1,2,3,4,5,6,7,8,9},
            ytick={0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9},
            tick align=inside,
            nodes near coords,
            %nodes near coords align=horizontal,
            ]
            \addplot table[x index=0, y index=1, col sep=comma,mark=none]
            {x.dat};
        \end{axis}
    \end{tikzpicture}
\end{document}

Answer 1

You can set the precision using /pgf/number format=3. To make the numbers fit, you can choose a smaller font and make the plot a bit wider. For nicer alignment, you can use anchor=-\coordindex*10, which will make the first node align with the 0 anchor (i.e. east), the second one with the -10 anchor (slightly below east), and so on.

\documentclass[12pt]{article}
\usepackage{tikz}
\usepackage{pgfplots}
\usepackage{filecontents}
\pagestyle{empty}

\begin{filecontents}{x.dat}
1,0.304313797
2,0.558012673
3,0.741302281
4,0.851281192
5,0.912940189
6,0.945961019
7,0.964838045
8,0.975736752
9,0.982694892
\end{filecontents}

\begin{document}
    \begin{tikzpicture}
        \begin{axis}[
            axis x line*=bottom,
            axis y line*=left,
            xlabel={Query Length},
            ylabel={Percentage},
            xmin=0,
            ymin=0,
            xmax=10,
            ymax=1,
            width=10cm, height=6cm,
            xtick={0,1,2,3,4,5,6,7,8,9},
            ytick={0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9},
            tick align=inside,
            nodes near coords,
            every node near coord/.append style={
                font=\scriptsize,
                /pgf/number format/precision=3,
                anchor=-\coordindex*10}
            ]
            \addplot table[x index=0, y index=1, col sep=comma,mark=none]
            {x.dat};
        \end{axis}
    \end{tikzpicture}
\end{document}