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}
I am definitely unfamiliar with both beamer and tikz (do not quite get what the \only are supposed to do) but perhaps this could go in the direction you want:
\documentclass{beamer}
\usepackage{tikz}
\usetikzlibrary{chains}
\newcounter{count}
% helper macro:
\long\def\GobToSemiColon #1;{}
\newcommand\myPicture{
\begin{tikzpicture}
\begin{scope}[start chain = going below]
\ifnum\value{count}<1 \expandafter\GobToSemiColon\fi
\ifnum\value{count}>3 \expandafter\GobToSemiColon\fi
\node[draw, rectangle, on chain] {display only when counter is between
1 and 3};
\ifnum\value{count}>-1 \expandafter\GobToSemiColon\fi
\node[draw, rectangle, on chain] {display only when counter is
negative};
\ifnum\value{count}<100 \expandafter\GobToSemiColon\fi
\ifnum\value{count}>200 \expandafter\GobToSemiColon\fi
\node[draw, rectangle, on chain] {display only if counter is between
100 and 200};
\ifnum\value{count}<3 \expandafter\GobToSemiColon\fi
\ifnum\value{count}>20 \expandafter\GobToSemiColon\fi
\node[draw, circle, on chain] {only when counter is in the range 3 to 20};
\end{scope}
\end{tikzpicture}
}
\begin{document}
\begin{frame}
\only{\setcounter{count}{-3}\myPicture}
\only{\setcounter{count}{105}\myPicture}
\only{\setcounter{count}{39}\myPicture}
\only{\setcounter{count}{2}\myPicture}
\only{\setcounter{count}{5}\myPicture}
\end{frame}
\end{document}
Best Answer
It seems like this works:
It seems that it is ok to use regular tikz code inside
\pgfdeclareplotmark. It may be horribly wrong, though, and could break any number of other things, so please use it with caution.