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On all platforms, you can generate PDF files directly using pdf(), or copy your graph from a screen device to a PDF file using dev.copy2pdf(). On Windows and Mac OS X, you can save your graphs directly from the windows() or quartz() screen devices to PDF files. Last but not least, you can easily export several graphs into a single PDF file. Each graph will be rendered on a separate page in the document.

Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace runs on practically any version of Unix-like OS. As well, it has been successfully ported to VMS, OS/2, and Win9*/NT/2000/XP (some minor functionality may be missing, though).

To make a density map from a 2D set of data, the first step is to compute values for the third dimension. (Gnuplot has no facilities for computing these values automatically.) The simplest way is to make a 2D histogram; the plot is divided in small 2D regions, and the z-values are proportional to the number of points inside these regions. The following Python script will make an histogram from a time series of two dihedral angles.