When eps created with matplotlib is displayed without problems with dvi, but the position of the image shifts when converted to pdf with dvipdfmx.
Since the cause and the conditions of the environment in which it occurs are completely unknown, only the solutions found by chance are introduced.
\usepackage{graphicx}
To
\usepackage[dvipdfmx]{graphicx}
change to
http://mkacky.wordpress.com/2013/05/27/tex%E3%81%A7dvi%E3%81%8B%E3%82%89pdf%E3%82%92%E4%BD%9C%E6%88%90%E3%81%99%E3%82%8B%E3%81%A8%E5%9B%B3%E3%81%8C%E3%81%9A%E3%82%8C%E3%82%8B/ The method introduced in did not work due to an error in Ghostscript.
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