[Tex/LaTex] PGF colorbar cuts off max value

pgfplotstikz-pgf

I need to generate a whole load of colorbars with custom min and max values.

From reading this SE I have managed to get this working:

\documentclass{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}
\begin{document}
\begin{tikzpicture}
\begin{axis}[
    hide axis,
    scale only axis,
    height=0pt,
    width=0pt,
    colormap/jet,
   colorbar,
   point meta min=0.0,
   point meta max=0.2860,
    colorbar style={ height= 10 cm},xtick={0,0.2860}]
    \addplot [draw=none] coordinates {(0,0)};
\end{axis}
\end{tikzpicture}

\end{document}

which produces this:

broken colorbar

It cuts off the top of the colorbar including the max value.

1) Why is this and how can I fix it?

2) How can I make the scale so it just has the min and max values?

Thanks

Best Answer

You have two problems: - standalone packages, which without defined border, for example border=5mm is (to) close to border of picture; - y range of your picture. If you set `point meta max=0.3, than the maximal value of your plot will appear.

\documentclass[border=5mm]{standalone}
    \usepackage{pgfplots}
\pgfplotsset{compat=newest}
    \begin{document}
\begin{tikzpicture}
\begin{axis}[
    hide axis,
    scale only axis,
    height=0pt,
    width=0pt,    
    colormap/jet,
    colorbar,
    point meta min=0.0,
    point meta max=0.2860,
    colorbar style={height=4cm,
            /pgf/number format/precision=3,
            ytick={0,0.286}}]
    \addplot [draw=none] coordinates {(0,0)};
\end{axis}
\end{tikzpicture}
    \end{document}

For how to put only min and max value o your diagram, I don't know.

Edit: Considering comment of @Grimler, you can obtain:

enter image description here

Now the my MWE is complete ...

ROOT data export

Before, I generated the scatter plot values via ROOT's Python bindings as:

import csv

def th2f_to_csv(hist, csv_file):
    """Print TH2F bin data to CSV file."""
    xbins, ybins = hist.GetNbinsX(), hist.GetNbinsY()
    xaxis, yaxis = hist.GetXaxis(), hist.GetYaxis()
    with open(csv_file, 'w') as f:
        c = csv.writer(f, delimiter=' ', lineterminator='\n')
        for xbin in xrange(xbins+2):
            xcenter = xaxis.GetBinCenter(xbin)
            for ybin in xrange(ybins+2):
                ycenter = yaxis.GetBinCenter(ybin)
                weight = hist.GetBinContent(xbin, ybin)
                if weight > 0:
                    c.writerow((xcenter, ycenter, weight))

The input argument hist is a TH2F object. See the ROOT and PyROOT documentation for more information.

The "+2" in xrange handles that ROOT saves an underflow and an overflow bin on top of the bins that are actually drawn. I at this stage explicitly threw out the points with no content to keep the "scatter plot" in PGFPlots clean.

But now I instead want to output a complete matrix, which I did as follows:

import csv

def th2f_to_csv(hist, csv_file):
    """Print TH2F bin data to CSV file."""
    xbins, ybins = hist.GetNbinsX(), hist.GetNbinsY()
    xaxis, yaxis = hist.GetXaxis(), hist.GetYaxis()
    with open(csv_file, 'w') as f:
        c = csv.writer(f, delimiter=' ', lineterminator='\n')
        for ybin in xrange(1, ybins+2):
            y_lowedge = yaxis.GetBinLowEdge(ybin)
            for xbin in xrange(1, xbins+2):
                x_lowedge = xaxis.GetBinLowEdge(xbin)
                weight = hist.GetBinContent(xbin, ybin)
                c.writerow((x_lowedge, y_lowedge, weight))

I now discard the underflow bin by starting the range from 1, and I also discard the overflow bin, since the last bin will not be shown when choosing shader=flat corner in PFDPlots later. I could have just given a dummy value instead of the actual overflow value, but it does not matter (EDIT: actually, it might matter if the overflow value is larger/smaller than the maximum/minimum "real" value — it would then affect the color map scale, so beware).

Instead of extracting the center of the bins, I now am interested in the lower bin edges.

I also change the order of the x and y loops to get the matrix data in a form that PGFPlots processes more efficiently, as described in section 7.2.1 in the manual: "Importing Mesh Data From Matlab To PGFPlots". This made a noticeable difference in compilation time.

Working examples

Now that I have the matrix, a minimal working example of plotting this data (matrix.csv) as a 2D histogram was:

\documentclass{article}

\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}

\begin{document}

\begin{tikzpicture}
  \begin{axis}[
    view={0}{90},
    colorbar,
  ]
    \addplot3[
      surf,
      shader=flat corner,
      mesh/cols=51,
      mesh/ordering=rowwise,
    ] file {matrix.csv};
  \end{axis}
\end{tikzpicture}

\end{document}

Minimum working example.

Section 7.2.1 in the manual and the earlier linked question explains the parameters. mesh/cols=51 comes from the known fact that the histogram contains 50 horizontal bins, and the extra one accounts for the "dummy bin" mentioned in the above linked TeX.SE question. The bin count could be output to a CSV specific configuration file along with the data if more automation is needed.

One issue was that the compiler (xelatex in this case) threw exactly 5000 rows to the terminal with content:

pgfplotsplothandlermesh@get@flat@color

There should be 50⨯100 = 5000 "cells" to be rendered in total in the image. This excess of messages might be a bug in itself, or something that I could have suppressed in some way.

Another issue is that the "background", i.e. the parts of the graph that represents value zero, is colored in, which is not optimal. The most obvious solution to this I found was to create a color map that "began" at white, which makes sense for these types of graphs anyway.

Along with some minor other formatting fixes, this gave the following result:

\documentclass{article}

\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}
\usepackage{siunitx}

\begin{document}

\pgfplotsset{
  /pgfplots/colormap={coldredux}{
    [1cm]
    rgb255(0cm)=(255,255,255)
    rgb255(2cm)=(0,192,255)
    rgb255(4cm)=(0,0,255)
    rgb255(6cm)=(0,0,0)
  }
}

\begin{tikzpicture}
  \begin{axis}[
    view={0}{90},
    xlabel={$\theta$ /degrees},
    ylabel={Energy /\si{\MeV}},
    minor tick num=4,
    colorbar,
    colorbar style={ylabel={Counts}},
  ]
    \addplot3[
      surf,
      shader=flat corner,
      mesh/cols=51,
      mesh/ordering=rowwise,
      x filter/.code={\pgfmathparse{#1*180}\pgfmathresult},
      y filter/.code={\pgfmathparse{#1/1000}\pgfmathresult},
    ] file {matrix.csv};
  \end{axis}
\end{tikzpicture}

\end{document}

Graphically updated version of histogram.

I will implement the x filter and y filter transformations in the analysis stage instead of the plotting stage.

Probably not a finished "product" yet, but now I can apply styling freely, and it is produced with a definitely manageable amount of code.

[Tex/LaTex] How to hide empty (value 0) ybars with pgfplots

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

Related Solutions

[Tex/LaTex] Building a 2D histogram with PGFPlots

ROOT data export

Working examples

[Tex/LaTex] How to hide empty (value 0) ybars with pgfplots

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