I was able to produce the figure with the non-trivial colormap by computing the coordinates and colors externally and using the meta point information in pgfplots. Here is the code:
\documentclass[tikz]{standalone}
\usepackage{tikz}
\usepackage{pgfplots}
\usetikzlibrary{calc}
\pgfplotsset{compat=1.8}
\begin{document}
\begin{tikzpicture}
\begin{scope}[yshift=0cm]
\draw[->, >=latex, color=black, line width=1.0pt, cap=round] (0.00, 0.00) -- (3.5, 0.00);
\draw[->, >=latex, color=black, line width=1.0pt, cap=round] (0.00, -1.00) -- (0.0, 1.00);
\begin{axis}[x=3cm, y=1cm, ticks=none, axis lines=none, colormap/jet, anchor=origin]
\addplot[mesh, ultra thick, point meta=\thisrow{c}, shader=interp] table[x=t, y=x] {sine_wave_high_res_01.dat};
\end{axis}
\end{scope}
\begin{scope}[xshift=5.0cm, yshift=0cm]
\draw[->, >=latex, color=black, line width=1.0pt, cap=round] (-1.10, 0.00) -- (1.25, 0.00);
\draw[->, >=latex, color=black, line width=1.0pt, cap=round] (0.00, -1.10) -- (0.0, 1.10);
\begin{axis}[x=0.2cm, y=0.2cm, ticks=none, axis lines=none, colormap/jet, anchor=origin]
\addplot[mesh, ultra thick, point meta=\thisrow{c}, shader=interp] table[x=x, y=y] {spiral_high_res_01.dat};
\end{axis}
\end{scope}
\end{tikzpicture}
\end{document}
