How to Produce TikZ Plots for Scientific Publications?

Getting nice plots for scientific publications is not optional.

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833#pcbi.1003833-Tufte1

figure;
x=[1:0.01:10];
plot(x,sin(x));
xlabel('x');
ylabel('sin(x)');

matlab2tikz(sprintf('./output/gt_power_iteration.tex'),'showInfo', false, ...
        'parseStrings',false,'standalone', false, ...
        'height', '\figureheight', 'width','\figurewidth');

\tikzset{font=\footnotesize}
\begin{tikzpicture}
 
every x tick label/.append style={font =\footnotesize},
every y tick label/.append style={font =\footnotesize},

f=figure;
boxplot([cum_ee_power_vector_per_user cum_gt_power_vector_per_user cum_maxlog_power_vector_per_user ...
    cum_pmax_power_vector_per_user cum_ee_nointerf_power_vector_per_user], 'notch', 'off');
set(gca,'xtick',1:5, 'xticklabel',{'Central-EE', 'Distributed-EE', 'Central-SE', 'Max-Power',  'EE-NoInterference'})
ylabel('Power (W)');
cleanfigure;
print(f,'-depsc', sprintf('./output/heur-boxplot-power%s.eps', figure_file_name));
savefig(sprintf('./output/heur-boxplot-power%s.fig', figure_file_name));
matlab2tikz(sprintf('./output/heur-boxplot-power%s.tex', figure_file_name),'showInfo', false, ...
        'parseStrings',false,'standalone', false, ...
        'height', '\figureheight', 'width','\figurewidth');

\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}
\usetikzlibrary{plotmarks}
\usepackage{grffile}
 
\newlength\figureheight
\newlength\figurewidth
 
\begin{figure}[!h]
	\centering
	\setlength\figureheight{0.3\textwidth}
	\setlength\figurewidth{0.35\textwidth}
	\input{figures/matlab-fig-tikz/central-dist-boxplot-objective-10users-7sectors-15RBs-20W.tex}
	\caption{Energy efficiency of the centralized and distributed approaches}
	\label{fig:central-dist-boxplot-objective-10users-7sectors-15RBs-20W}
\end{figure}