Hi Joshua,
as already mentioned, your old mails from January have slipped my
discipline... I am sorry for not answering right away. I should have
written "sorry, I am busy please also try tex.stackexchange" after there
was no answer for some time.
You asked for a simpler way to
a) position groups of bars without having to compute 'bar shift' manually
b) a simpler way to get "significance stars".
First, grouped bar charts are an open feature request in pgfplots, and
your input will eventually prove to be valueable as definition of
requirements. I haven't thought much on significance stars so far; I
fear your current solution which fixes the y location is the best at
hand. There may be ways to write complicated styles which implement that
feature, but that's clearly advanced.
The first request is actually possible, assuming that you always provide
them in the sequence as you did: I copied the default definition of 'bar
shift' and adopted it.
The default is
/pgfplots/ybar/.style={
/pgf/bar shift={%
% total width = n*w + (n-1)*skip
% -> subtract half for centering
-0.5*(\numplotsofactualtype*\pgfplotbarwidth +
(\numplotsofactualtype-1)*#1) +
% the '0.5*w' is for centering
(.5+\plotnumofactualtype)*\pgfplotbarwidth +
\plotnumofactualtype*#1},%
}
and my modification substitutes every index and 'n' by half of it:
\pgfplotsset{
% #1 = separation between bars
bar shift for half number plots/.style={%
/pgf/bar shift={%
% total width = n*w + (n-1)*skip
% -> subtract half for centering
-0.5*(\numplotsofactualtype/2*\pgfplotbarwidth +
(\numplotsofactualtype/2-1)*#1) +
% the '0.5*w' is for centering
(.5+div(\plotnumofactualtype,2))*\pgfplotbarwidth +
div(\plotnumofactualtype,2)*#1%
},%
},%
bar shift for half number plots/.default=2pt,
}
With this definition, you do not have to write 'bar shift' in your styles.
The whole figure becomes
\usemodule[pgfplots]
\pgfplotsset{compat=newest}
\pgfplotsset{HeartControl/.style=
{
red, fill=red!33!white,
%bar shift=-0.1667
}}
\pgfplotsset{HeartDiabetes/.style=
{
red!33!black, fill=red!66!white,
%bar shift=+0.1667
}}
\pgfplotsset{KidneyControl/.style=
{
orange, fill=orange!33!white,
%bar shift=-0.1667
}}
\pgfplotsset{KidneyDiabetes/.style=
{
orange!33!black, fill=orange!66!white,
%bar shift=+0.1667
}}
\pgfplotsset{/pgfplots/ybar legend/.style=
{
/pgfplots/legend image code/.code={%
\draw[
##1, /tikz/.cd,
bar width=0.25em,
yshift=-0.27em,
bar shift=0pt
]
plot coordinates {(0pt,0.8em)};
}
}}
\pgfplotsset{
% #1 = separation between bars
bar shift for half number plots/.style={%
/pgf/bar shift={%
% total width = n*w + (n-1)*skip
% -> subtract half for centering
-0.5*(\numplotsofactualtype/2*\pgfplotbarwidth +
(\numplotsofactualtype/2-1)*#1) +
% the '0.5*w' is for centering
(.5+div(\plotnumofactualtype,2))*\pgfplotbarwidth +
div(\plotnumofactualtype,2)*#1%
},%
},%
bar shift for half number plots/.default=2pt,
}
\starttext
\starttikzpicture
\startaxis
[
bar width=0.3,
ybar,
bar shift for half number plots=5pt,
xtick=data,
ylabel={mRNA level},
ymin=0,
xmin=0.333, xmax=2.667,
xtick={1,2}, xticklabels={Heart,Kidney},
error bars/y dir=both,
error bars/y explicit,
legend columns=2,
legend pos=outer north east,
legend cell align=left
]
\addplot+[HeartControl] coordinates {(1,1) +- (0,0.1)};
\addplot+[KidneyControl] coordinates {(2,1) +- (0,0.12)};
\addplot+[HeartDiabetes] coordinates {(1,1.1) +- (0,0.2)};
\addplot+[KidneyDiabetes] coordinates {(2,0.8) +- (0,0.05)};
\draw (axis cs:2,1.15) +(-2.2em,0) -- +(2.2em,0);
\node[anchor=south, yshift=-1ex] at (axis cs:2,1.15) {*};
\legend{{\kern-0.1em}, Control, {\kern-0.1em}, Diabetes}
\stopaxis
\stoptikzpicture
\stoptext
I suppose you could even simplify the styles by means of a cycle list or
whatever.
I also experimented with symbolic x coords, but how would you write
"xmin=0.3333" or "bar width=0.3" (which are axis units)? I believe the
solution with arbitrary constants is better (i.e. as you have it right now).
You can use
\def\heartUnit{1}
\def\kidneyUnit{2}
to introduce constants - this might make it more readable.
I am aware of the fact that this solution comes way too late. Perhaps it
proves to be useful for someone eventually.
Kind regards
Christian
Am 21.01.2014 13:29, schrieb Joshua Krämer:
> Dear pgfplots developers!
>
> First, thanks a lot for your great package. I'm using it to create
> diagrams in ConTeXt. Please consider the following (M)WE. I hope you
> can run it, otherwise, you can see the output here:
> http://666kb.com/i/cl5sdm34i4ig69mkk.png
>
> \usemodule[pgfplots]
> \pgfplotsset{compat=newest}
>
> \pgfplotsset{HeartControl/.style=
> {
> red, fill=red!33!white,
> bar shift=-0.1667
> }}
> \pgfplotsset{HeartDiabetes/.style=
> {
> red!33!black, fill=red!66!white,
> bar shift=+0.1667
> }}
> \pgfplotsset{KidneyControl/.style=
> {
> orange, fill=orange!33!white,
> bar shift=-0.1667
> }}
> \pgfplotsset{KidneyDiabetes/.style=
> {
> orange!33!black, fill=orange!66!white,
> bar shift=+0.1667
> }}
>
> \pgfplotsset{/pgfplots/ybar legend/.style=
> {
> /pgfplots/legend image code/.code={%
> \draw[
> ##1, /tikz/.cd,
> bar width=0.25em,
> yshift=-0.27em,
> bar shift=0pt
> ]
> plot coordinates {(0pt,0.8em)};
> }
> }}
>
> \starttext
>
> \starttikzpicture
> \startaxis
> [
> ybar,
> xtick=data,
> ylabel={mRNA level},
> ymin=0,
> xmin=0.333, xmax=2.667,
> xtick={1,2}, xticklabels={Heart,Kidney},
> error bars/y dir=both,
> error bars/y explicit,
> bar width=0.3,
> legend columns=2,
> legend pos=outer north east,
> legend cell align=left
> ]
>
> \addplot+[HeartControl] coordinates {(1,1) +- (0,0.1)};
> \addplot+[KidneyControl] coordinates {(2,1) +- (0,0.12)};
> \addplot+[HeartDiabetes] coordinates {(1,1.1) +- (0,0.2)};
> \addplot+[KidneyDiabetes] coordinates {(2,0.8) +- (0,0.05)};
>
> \draw (axis cs:2,1.15) +(-2.2em,0) -- +(2.2em,0);
> \node[anchor=south, yshift=-1ex] at (axis cs:2,1.15) {*};
>
> \legend{{\kern-0.1em}, Control, {\kern-0.1em}, Diabetes}
>
> \stopaxis
> \stoptikzpicture
>
> \stoptext
>
> As you can see, I have two groups (organs: hearts, kidneys), sometimes
> more, and two conditions (control, Diabetes). To make it easier to
> compare the diagrams (there are many), I want to use consistent colours
> for the same organs, and two brightnesses for the two conditions. The
> code above works, but automatic positioning would be much nicer, so I
> could just set something like "bar width=..." and "bar seperation=..."
> and let the bars be positioned automatically. This would also allow me
> to use symbolic coordinates, avoiding the pseudo coordinates (1 and
> 2). Is there a better way to get the desired result than what I've
> done?
>
> I also hope there is a better way to create significance stars. If two
> values are significantly different, there is a horizontal line to be
> added which spans the two bars, and a symbol above it. The symbols
> usually are one till three stars (depending on the degree of
> significance), sometimes other symbols are used in the literature. At
> least it would be nice if I could define the coordinates for the
> horizontal line with something like "max(errormark1, errormark2) +a",
> ie, the higher of the two error marks involved plus some separation.
>
> Kind regards,
> Joshua Krämer
>
>
>
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