You can use
y filter/.expression={y==0 ? nan : y}
in the options of \addplot.
\documentclass{article}
% ---------------------------------- tikz
\usepackage{pgfplots} % to print charts
\pgfplotsset{compat=1.12}
\begin{document}
\begin{figure}
\centering
\begin{tikzpicture}
\begin{axis} [
% general
ybar,
scale only axis,
height=0.5\textwidth,
width=1.2\textwidth,
ylabel={\# Dots},
nodes near coords,
xlabel={Variation},
xticklabel style={
rotate=90,
anchor=east,
},
%enlarge x limits={abs value={3}},
]
\addplot+[y filter/.expression={y==0 ? nan : y}] table [
x=grade,
y=value,
] {
grade value
-11 0
-10 0
-9 0
-8 0
-7 0
-6 0
-5 3
-4 1
-3 2
-2 15
-1 11
0 179
1 8
2 1
3 0
4 1
5 2
6 0
7 0
8 0
9 0
10 0
11 0
};
\end{axis}
\end{tikzpicture}
\end{figure}
\end{document}
It does not work in your MWE because you are overwriting it by also giving the option nodes near coors to the \addplot command. Remove the latter one (or specify format here), and it will print. I added a thinspace before the percentage sign, although it can also be recommended to load the siunitx package and let that format and typeset the values for you.
Anyway, here's the quickfixed version:
\documentclass[border=3pt]{standalone}
\usepackage{pgfplots}
\pgfplotsset{%
width=5cm,
height=18cm,
compat=1.13,
colormap={blackwhite}{gray(0cm)=(1); gray(1cm)=(0.5)},
xticklabels={LPIBG, ALL, HPIBG},
xtick={0,...,2},
ytick=\empty
}
\begin{document}
\begin{tikzpicture}
\begin{axis}[%
enlargelimits=false,
xlabel style={font=\footnotesize},
ylabel style={font=\footnotesize},
legend style={font=\footnotesize},
xticklabel style={font=\footnotesize},
yticklabel style={font=\footnotesize},
colorbar,
colorbar style={%
ytick={0,20,40,60,80,100},
yticklabels={0,20,40,60,80,100},
yticklabel={\pgfmathprintnumber\tick\,\%},
yticklabel style={font=\footnotesize}
},
point meta min=0,
point meta max=100,
nodes near coords={\pgfmathprintnumber\pgfplotspointmeta\,\%},
every node near coord/.append style={xshift=0pt,yshift=-7pt, black, font=\footnotesize},
]
\addplot[
matrix plot,
mesh/cols=3,
point meta=explicit]
table[meta=C]{
x y C
0 0 80
1 0 36
2 0 40
0 1 64
1 1 80
2 1 60
0 2 52
1 2 84
2 2 72
0 3 72
1 3 28
2 3 32
0 4 56
1 4 84
2 4 80
0 5 72
1 5 52
2 5 44
0 6 4
1 6 84
2 6 41
0 7 37
1 7 69
2 7 84
0 8 63
1 8 53
2 8 82
0 9 78
1 9 74
2 9 39
0 10 39
1 10 63
2 10 88
0 11 76
1 11 74
2 11 49
0 12 39
1 12 6
2 12 88
0 13 46
1 13 33
2 13 75
0 14 88
1 14 67
2 14 54
0 15 79
1 15 83
2 15 75
0 16 50
1 16 46
2 16 71
0 17 92
1 17 71
2 17 75
0 18 46
1 18 33
2 18 8
};
\end{axis}
\end{tikzpicture}
\end{document}
Best Answer
My approach would be to just use major ticks, and to specify explicitly which ones you need. You can use
...in the list of ticks and their labels. I admit that it's kind of repetitive, but I don't know whether it is possible to shorten this syntax further (in a reasonable way). For two decades (as in your example) it's ok I guess.