This happens because PGFPlots only uses one "stack" per axis: You're stacking the second confidence interval on top of the first. The easiest way to fix this is probably to use the approach described in "Is there an easy way of using line thickness as error indicator in a plot?": After plotting the first confidence interval, stack the upper bound on top again, using stack dir=minus
. That way, the stack will be reset to zero, and you can draw the second confidence interval in the same fashion as the first:

\documentclass{standalone}
\usepackage{pgfplots, tikz}
\usepackage{pgfplotstable}
\pgfplotstableread{
temps y_h y_h__inf y_h__sup y_f y_f__inf y_f__sup
1 0.237340 0.135170 0.339511 0.237653 0.135482 0.339823
2 0.561320 0.422007 0.700633 0.165871 0.026558 0.305184
3 0.694760 0.534205 0.855314 0.074856 -0.085698 0.235411
4 0.728306 0.560179 0.896432 0.003361 -0.164765 0.171487
5 0.711710 0.544944 0.878477 -0.044582 -0.211349 0.122184
6 0.671241 0.511191 0.831291 -0.073347 -0.233397 0.086703
7 0.621177 0.471219 0.771135 -0.088418 -0.238376 0.061540
8 0.569354 0.431826 0.706882 -0.094382 -0.231910 0.043146
9 0.519973 0.396571 0.643376 -0.094619 -0.218022 0.028783
10 0.475121 0.366990 0.583251 -0.091467 -0.199598 0.016664
}{\table}
\begin{document}
\begin{tikzpicture}
\begin{axis}
% y_h confidence interval
\addplot [stack plots=y, fill=none, draw=none, forget plot] table [x=temps, y=y_h__inf] {\table} \closedcycle;
\addplot [stack plots=y, fill=gray!50, opacity=0.4, draw opacity=0, area legend] table [x=temps, y expr=\thisrow{y_h__sup}-\thisrow{y_h__inf}] {\table} \closedcycle;
% subtract the upper bound so our stack is back at zero
\addplot [stack plots=y, stack dir=minus, forget plot, draw=none] table [x=temps, y=y_h__sup] {\table};
% y_f confidence interval
\addplot [stack plots=y, fill=none, draw=none, forget plot] table [x=temps, y=y_f__inf] {\table} \closedcycle;
\addplot [stack plots=y, fill=gray!50, opacity=0.4, draw opacity=0, area legend] table [x=temps, y expr=\thisrow{y_f__sup}-\thisrow{y_f__inf}] {\table} \closedcycle;
% the line plots (y_h and y_f)
\addplot [stack plots=false, very thick,smooth,blue] table [x=temps, y=y_h] {\table};
\addplot [stack plots=false, very thick,smooth,blue] table [x=temps, y=y_f] {\table};
\end{axis}
\end{tikzpicture}
\end{document}
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}

Best Answer
Probably Till Tantau was having similar problems so he created the error messages in a smarter way. Example; if I go something like this
The error message is
Now your example; let's read the error message
Notice that it doesn't say you tried to pass
bottom
it says that it didn't understand the whole thing. Because it didn't parse it and missed the equation sign and the value you have provided. You can get more stupid cases such asThese all tell that PGF keys didn't expand it properly. One immediate thing is to manually expand the argument by delaying the expandion of
\pgfplotsset{
partwould work. Or you can still stay within PGF keys and use the
/.expanded
handler which does the expansion for you.What does this do? First,
/utils/exec
is the general handler for executing arbitrary TeX code. Then by just identifying what should not be expanded, here\pgfplotsset
and adding\noexpand
before them, you can set any kind of macro values.You can also control how many times it should expand and you can check the manual for
expand once
andexpand twice
keys for that.