Plotting

• Label axes and indicate measurement units when available
• Give your figures meaningful titles
• Avoid low contrast color combinations (such as yellow, pink, cyan, and bright green on white) for better display over projector and on printing
• Use very large font when you want to show figures over projector or on paper
• Maximize data-to-ink ratio on your plots
• When comparing several lines in one plot use different colors and line types (solid, dotted, dash) and add an explanatory legend
• Scale axes so that data takes most of the space
• Add error bars
• Export data to .eps format and edit in Abode Illustrator/Inkscape for publication quality
• Use luminance- or saturation-based colormaps instead of hue-based ones, which are default in many software packages (detailed explanation)
• Avoid chartjunk
• Use transparent background
• Some good tips for generating pretty figures in MATLAB here