\documentclass{article}

%Minted for syntax hightlighting
\usepackage{minted}

%These are for plots
\usepackage{pgfplots}
\usepackage{fontspec}
\setmainfont{TeX Gyre Pagella}
\usepackage{amsmath}
\usepackage[active,tightpage]{preview}

%Hyperlinks
\usepackage{hyperref}
\hypersetup{colorlinks=true, urlcolor=blue}
%Some style changes
\setlength{\parindent}{0in}
\setlength{\parskip}{12pt}


\author{Matti Pastell}
\title{Using PGF plots with Weave and Gadfly}

\begin{document}


\maketitle

\section{Intro}

This is a minimal example on using PGF format with Gadfly plots in
\href{https://github.com/JunoLab/Weave.jl}{Weave.jl} document.
The source is in github:

\url{https://github.com/JunoLab/Weave.jl/blob/master/examples/gadfly_pgf.texw}.

You can run this example with first weaving it from Julia using:

<<eval=false>>=
using Weave
weave(Pkg.dir("Weave", "examples", "gadfly_pgf.texw"),
    doctype="texminted", out_path=:pwd, fig_ext=".tex")
@

which will save the generated output in your working directory and use minted
package for syntax hightlighting. You'll need to use either xetex or luatex with
\texttt{-shell-escape} flag to get pdf e.g.

\begin{minted}{bash}
lualatex -shell-escape gadfly_pgf.tex
\end{minted}

\section{Sample code}

You can set the default font in Gadfly to match the font in the document.
Use the \texttt{fontspec} latex package (see preamble) and define the
defaults to Gadfly as follows.

If you want you can hide the chunk using the \texttt{echo=false} chunk option.

<<>>=
using Gadfly
Gadfly.default_theme.major_label_font = "Tex Gyre Pagella"
Gadfly.default_theme.minor_label_font = "Tex Gyre Pagella"
Gadfly.default_theme.major_label_color = colorant"black"
Gadfly.default_theme.minor_label_color = colorant"black"
@

Let's create a simple plot:

<<>>=
x = 1:10
plot(x=x, y=x)
@

And a figure with a caption

<<fig_cap="Nice Gadfly figure">>=
plot([sin, cos], 0, 25)
@


\end{document}