[Tex/LaTex] Why are some of the boxplots dashed

boxplotpgfplots

Here's a MWE:

\documentclass[a4paper]{standalone}

\usepackage{pgfplots}
\usepgfplotslibrary{statistics}
\pgfplotsset{compat=1.8}

\begin{document}

\begin{tikzpicture}
\begin{axis}[
boxplot/draw direction=y,
ylabel={root mean square error (RMSE)},
height=8cm,
boxplot={
    %
    % Idea: 
    %  place the 
    %  group 1 at 0.3333 and 0.6666
    %  group 2 at 1.3333 and 1.6666
    %  group 3 at 2.3333 and 2.6666
    %  ...
    % in a formular:
    draw position={1/3 + floor(\plotnumofactualtype/2) + 1/3*mod(\plotnumofactualtype,2)},
    %
    % that means the box extend must be at most 0.33333 :
    box extend=0.3
},
% ... it also means that 1 unit in x controls the width:
x=2cm,
% ... and it means that we should describe intervals:
xtick={0,1,2,...,10},
x tick label as interval,
xticklabels={%
    {dataset 1\\{\tiny disabled enabled}},%
    {dataset 2\\{\tiny disabled enabled}},%
    {dataset 3\\{\tiny disabled enabled}},%
    {dataset 4\\{\tiny disabled enabled}},%
},
    x tick label style={
        text width=2.5cm,
        align=center
    },
]


%disabled
%'120689': [2.7646732338376374, 2.9386338075128915, 2.0759453040402924, 1.4933341587154352, 1.2858810574360171], 
%'123092': [1.6213436825515752, 3.659127461813457, 6.3573913630881957, 2.851522397932257, 1.4161184310137278]
%'122034': [2.7782786785170344, 2.388295853323815, 1.0169391397932168, 1.3282220840941463, 1.1519878464320008], 
%'overd': [1.4050751524256098, 1.1888905444333131, 4.330757692491046, 3.665914730249296, 1.4398896445581748], 

%enabled
%'120689': [1.1753863748576165, 2.8136463510466894, 2.0065471893571609, 3.8938997085167464, 2.0129749752740276], 
%'123092': [2.2803725936262524, 1.4825727354215965, 1.7871388688900045, 2.3261434769789657, 1.795254324625537]
%'122034': [1.0286497508188084, 1.5717822303817375, 4.0903690748471373, 3.8755839151245763, 1.8905509506317051], 
%'overd': [2.9370285732792341, 1.3202361917111065, 1.3576990603035917, 1.852324571876895, 1.2151847831011142], 

\addplot
table[row sep=\\,y index=0] {
data\\
2.764\\
2.938\\
2.075\\
1.493\\
1.285\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.175\\
2.813\\
2.006\\
3.893\\
2.012\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.621\\
3.659\\
6.357\\
2.851\\
1.416\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
2.280\\
1.482\\
1.787\\
2.326\\
1.795\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
2.778\\
2.388\\
1.016\\
1.328\\
1.151\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.028\\
1.571\\
4.090\\
3.875\\
1.890\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.405\\
1.188\\
4.330\\
3.665\\
1.439\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
2.937\\
1.320\\
1.357\\
1.852\\
1.215\\
};

\end{axis}
\end{tikzpicture}


\end{document}

Why are the last three boxplots dashed?

what-the-hell

Sorry that there's still so much code in the MWE, it's just that the dashed boxplots don't appear if I try to make the MWE smaller. :/

Best Answer

As @darthbith said in his comment to my question:

At a guess, its due to the cycle lists that pgfplots uses to pick the line styles. See page 173 of the 1.10 manual. – darthbith 7 hours ago

Therefore, I took control of the cycle list (and added ymin/ymax values) to let the plot behave as I had originally intended, by adding line 15, cycle list={{red},{blue}},.

MWE:

\documentclass[a4paper]{standalone}

\usepackage{pgfplots}
\usepgfplotslibrary{statistics}
\pgfplotsset{compat=1.8}

\begin{document}

\begin{tikzpicture}
\begin{axis}[
boxplot/draw direction=y,
ylabel={RMSE},
height=6cm,
ymin=0,ymax=7,
cycle list={{red},{blue}},
boxplot={
        %
        % Idea: 
        %  place the 
        %  group 1 at 0.3333 and 0.6666
        %  group 2 at 1.3333 and 1.6666
        %  group 3 at 2.3333 and 2.6666
        %  ...
        % in a formular:
        draw position={1/3 + floor(\plotnumofactualtype/2) + 1/3*mod(\plotnumofactualtype,2)},
        %
        % that means the box extend must be at most 0.33333 :
        box extend=0.3
},
% ... it also means that 1 unit in x controls the width:
x=2cm,
% ... and it means that we should describe intervals:
xtick={0,1,2,...,10},
x tick label as interval,
xticklabels={%
        {dataset 1\\{\tiny disabled enabled}},%
        {dataset 2\\{\tiny disabled enabled}},%
        {dataset 3\\{\tiny disabled enabled}},%
        {dataset 4\\{\tiny disabled enabled}},%
},
        x tick label style={
                text width=2.5cm,
                align=center
        },
]


%disabled
%'120689': [2.7646732338376374, 2.9386338075128915, 2.0759453040402924, 1.4933341587154352, 1.2858810574360171], 
%'123092': [1.6213436825515752, 3.659127461813457, 6.3573913630881957, 2.851522397932257, 1.4161184310137278]
%'122034': [2.7782786785170344, 2.388295853323815, 1.0169391397932168, 1.3282220840941463, 1.1519878464320008], 
%'overd': [1.4050751524256098, 1.1888905444333131, 4.330757692491046, 3.665914730249296, 1.4398896445581748], 

%enabled
%'120689': [1.1753863748576165, 2.8136463510466894, 2.0065471893571609, 3.8938997085167464, 2.0129749752740276], 
%'123092': [2.2803725936262524, 1.4825727354215965, 1.7871388688900045, 2.3261434769789657, 1.795254324625537]
%'122034': [1.0286497508188084, 1.5717822303817375, 4.0903690748471373, 3.8755839151245763, 1.8905509506317051], 
%'overd': [2.9370285732792341, 1.3202361917111065, 1.3576990603035917, 1.852324571876895, 1.2151847831011142], 

\addplot
table[row sep=\\,y index=0] {
data\\
2.764\\
2.938\\
2.075\\
1.493\\
1.285\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.175\\
2.813\\
2.006\\
3.893\\
2.012\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.621\\
3.659\\
6.357\\
2.851\\
1.416\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
2.280\\
1.482\\
1.787\\
2.326\\
1.795\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
2.778\\
2.388\\
1.016\\
1.328\\
1.151\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.028\\
1.571\\
4.090\\
3.875\\
1.890\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
1.405\\
1.188\\
4.330\\
3.665\\
1.439\\
};

\addplot
table[row sep=\\,y index=0] {
data\\
2.937\\
1.320\\
1.357\\
1.852\\
1.215\\
};

\end{axis}
\end{tikzpicture}


\end{document}

Output:

better

Related Solutions

[Tex/LaTex] Two boxplots per plot entry – shifting boxplots in pgfplots

In principle, you can just provide one or more box plots here. In your case, it appears to be boxplot prepared with suitable arguments.

I rarely had the opportunity to study common box plot styles, so I took the freedom to adopt pgfplots to your style. Maybe I can add such styles to pgfplots eventually, so feedback of sorts "I miss a style like XYZ" are welcome.

Anyway, I arrived at the following which appears to be quite close to what you want to archieve:

enter image description here

\documentclass{standalone}

\usepackage{pgfplots}
\usepgfplotslibrary{statistics}

\pgfplotsset{
    jja style/.style={
        % draw whiskers as a single line:
        boxplot/draw/whisker/.code 2 args={%
            \draw[/pgfplots/boxplot/every whisker/.try]
                (boxplot cs:##1) -- (boxplot cs:##2)
            ;
        },%
        %
        % fill the boxes:
        boxplot/every box/.style={
            fill,
        },
        % 
        % the median should be visualized as a circle:
        boxplot/draw/median/.code={%
            \draw[fill=white]
                (boxplot cs:\pgfplotsboxplotvalue{median}) circle (3pt)
            ;
        },
        %
        % do not clip to avoid problems with the median:
        clip=false,
        %
        boxplot/draw direction=y,
        %
        % configure axis lines:
        x axis line style={opacity=0},
        axis x line*=bottom,
        axis y line=left,
        %
        ymajorgrids,
        yminorgrids,
        minor y tick num=1,
        ytick={0,50,100},
        ylabel=\%,
        ylabel style={rotate=-90},
        %
        % width of boxes:
        boxplot/box extend=0.3,
    },
    %
    %
    rshift/.style={
        xshift=\pgfkeysvalueof{/pgfplots/rshift scale},
        legend image post style={xshift=-\pgfkeysvalueof{/pgfplots/rshift scale}},
        blue!70!black,
    },
    lshift/.style={
        xshift=-\pgfkeysvalueof{/pgfplots/lshift scale},
        legend image post style={xshift=\pgfkeysvalueof{/pgfplots/lshift scale}},
        orange,
    },
    rshift scale/.initial=1em,
    lshift scale/.initial=1em,
}
\begin{document}

\begin{tikzpicture}
\begin{axis}[
    jja style,
    ymin=0,
    ymax=100,
    xtick={1,2,3},
    xticklabels={isol,qfin,qint},
]
\addplot+[
    forget plot,
    rshift,
    boxplot prepared={
        lower whisker=27, lower quartile=45,
        median=59,
        upper quartile=61, upper whisker=70,
    },
]
    coordinates {};

\addplot+[
    lshift,
    boxplot prepared={
        lower whisker=100, lower quartile=100,
        median=100,
        upper quartile=100, upper whisker=100,
    },
]
    coordinates {};


\addplot+[
    forget plot,
    rshift,
    boxplot prepared={
        lower whisker=47, lower quartile=50,
        median=57,
        upper quartile=70, upper whisker=71,
    },
]
    coordinates {};
\addplot+[
    lshift,
    boxplot prepared={
        lower whisker=87, lower quartile=92,
        median=100,
        upper quartile=100, upper whisker=100,
    },
]
    coordinates {};
\end{axis}
\end{tikzpicture}

\end{document}

(my convert outputs used to be better; no idea why the quality of the screenshot looks so degenerate!?)

I do not know what you mean by "breaking my hack", but I would be interested in why and how pgfplots "broke" something. Breaking compatibility is surely something that it should not do, so I consider any problem of this sorts a bug report. I would appreciate it if you would send an email to me which illustrates the problem (some minimal working example).

[Tex/LaTex] pgfplots generating incorrect boxplots

There are at least two different factors potentially contributing to differences in the boxplots produced by Matlab and pgfplots.

1. `<=` and `>=` (Matlab) vs `<` and `>` (pgfplots)

There is a difference in the definitions of whiskers and outliers.

From the manual of pgfplots (I have emphasized the key fact):

lower whisker is the smallest data value which is larger than lower quartile−1.5 · IQR

and

upper whisker is the largest data value which is smaller than upper quartile+1.5 · IQR

From the manual of Matlab (emphasis added):

Points are drawn as outliers if they are larger than Q3+W*(Q3-Q1) or smaller than Q1-W*(Q3-Q1), where Q1 and Q3 are the 25th and 75th percentiles, respectively. The default value 1.5 corresponds to approximately +/- 2.7 sigma and 99.3 coverage if the data are normally distributed. The plotted whisker extends to the adjacent value, which is the most extreme data value that is not an outlier.

2. Different methods for computing box limits / quartiles

It would be all too easy to say that the box limits are the 1st and 3rd quartile (a.k.a. 25th and 75th percentile, a.k.a. quantiles with probabilities 0.25 and 0.75) and leave it at that. Alas, there are many methods for computing quantiles. Without going into too much detail, there are no less than 9 different quantile() method variants in R. For the example data set, these methods give 7 unique results for the pair of numbers (25th and 75th percentile). These are:

0 and 5
0.5 and 4.5
0.75 and 6.25
0.9166667 and 5.4166667
0.9375 and 5.3125
1 and 5
1.25 and 4.75

Matlab finds the box limits to be 1 and 5. According to @Jake (see comments), the limits in pgfplots are 1.5 and 4.5, which can also be approximately confirmed by looking at the picture attached by the original poster. Note that this corresponds to yet another definition of quantile. The pgfplots manual, Revision 1.11 (2014/08/04), states the following about the computation of quantiles:

pgfplots manual, about quantiles

I am not sure how exactly this maps the quartiles of the example data set to 1.5 and 4.5. We have x1=-9, x2=0, x3=1, x4=2, x5=x6=3, x7=4, x8=5, x9=10 and x10=14. Following the formula in the pgfplots manual, we get lower quartile 0.5*(x2+x3)=0.5*(0+1)=0.5 and upper quartile 0.5*(x7+x8)=0.5*(4+5)=4.5. One consequence of using the formula presented in the pgfplots manual is that for computing small quantiles, one would need the non-existent value x0.

How this works with the example data

Assuming what I wrote above is correct and everything works as documented, we can work through a boxplot of the example data from the perspective of both Matlab and pgfplots.

Matlab

Assuming that the quartiles are 1 and 5, the inter-quartile range (IQR) is 4. Now 1.5*IQR is 6. Third quartile + 1.5*IQR is 11. Data value 14 is larger than that which makes it an outlier. However, 10 is not an outlier. Thus the upper whisker extends to 10.

pgfplots

Assuming that the quartiles are 1.5 and 4.5, the inter-quartile range (IQR) is 3. Now 1.5*IQR is 4.5. Third quartile + 1.5*IQR is 9. Data value 14 is larger than that which makes it an outlier. Also 10 is an outlier. 5 is the largest number which is not an outlier. Thus the upper whisker extends to 5.

Conclusion

I cannot tell for sure which of the boxplot computation methods is better or correct. I can add another data point: In case of the example data, boxplot() in R gives the same result as Matlab.

One should also note that due to the limitations of computer arithmetics and the discrete nature of the whisker locations, different implementations using the same formula may also produce a different result depending on the data set.