jbmouret / matplotlib_for_papers Goto Github PK

I suggest to add Anaconda distribution - its very easy to install and the conda installer is great for numpy/scipy/etc.

I have been following the tutorial for the plotting and had issues with the glob function finding the bestfit.dat files. I used the files from data.tar.gz. The folder structure of the code does not match the folder structure of the compressed file. There is no data folder and the high_mut folder extracts as matplotlib_high_mut. These differences made it to where none of the data or plots were generated. I was able to correct the folder names and continue with the tutorial, but I feel that others may not have. Thank you- JT

It seems that there is a change in the new version of matplotlib and boxplot3.py, boxplot4.py and boxplo5.py do not work anymore:

/usr/lib/python2.7/dist-packages/matplotlib/init.py:874: UserWarning: text.fontsize is deprecated and replaced with font.size; please use the latter.
warnings.warn(self.msg_depr % (key, alt_key))
Traceback (most recent call last):
File "boxplot3.py", line 48, in
bp['fliers'][i * 2].set(markerfacecolor=colors[i],
IndexError: list index out of range

In boxplot3.py, the error can be addressed by making the following change. Replace lines 48-53 (https://github.com/jbmouret/matplotlib_for_papers/blob/master/src/boxplot3.py#L48) with just this:

bp['fliers'][i].set(markerfacecolor=colors[i],
marker='o', alpha=0.75, markersize=6,
markeredgecolor='none')

I'm using gnuplot in combination with gnuplottex to create all my graphs. It allows for an incredible easy and efficient workflow and allows me to typeset the text in my graphs using LaTeX. gnuplottex automates the process of generating a *.pdf containing the actual drawings in combination with a *.tex file including the drawing and overlaying the text at the appropriate positions using LaTeX.

1. Is it possible to generate *.tex/*.pdf combinations in a similar way, such that I can use LaTeX and all my document specific settings to typeset my text?
2. If so, is there something analog to gnuplottex in order to simplify the workflow?

For example, to generate the following output

I use the code below, ran with pdflatex just once.

\documentclass{article}

\usepackage[miktex]{gnuplottex}
\usepackage[pdftex]{color}

\begin{document}
    \begin{figure}[htbp]
        \footnotesize\centering
        \begin{gnuplot}[terminal=cairolatex, terminaloptions={color colortext pdf size 3,2}]
            load 'common.plt'

            set xtics 0, 1
            set ytics -1, 1
            set xrange [0:2*pi]
            set xlabel '$x$'
            set ylabel '$\sin(x)$'

            plot sin(x) title '$\sin(x)$'
        \end{gnuplot}
        \caption{$\sin(x)$}
    \end{figure}
\end{document}

we cannot use zip anymore in the boxplot, we need list(zip(...))

The link to the data for the "Data over time" section is dead. It points to your older website, namely http://chronos.isir.upmc.fr/~mouret/alife_matplotlib/src/data/data.tar.gz. It also seems that the data is not at your new website's location.

Maybe it would be better to make it part of the repository.