Nathan Yau of FlowingData offers recommendations to newcomers to data visualization, with his take on the appropriate visualization software/tool to use. He generally uses R combined with Illustrator, and so this is his recommendation for publication, presentation and analysis. Nathan also suggests alternatives: Tableau Software for analysis and Processing for web applications and art. (I'm not familiar with either of those myself, although I've been keen to check out Processing when I get time.)
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