Highcharts provides 20 different types of [charts](http://www.highcharts.com/docs/chart-and-series-types/chart-types) to choose from, and they make it simple to [combine](http://www.highcharts.com/docs/chart-and-series-types/combining-chart-types) chart types.
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Pergola runs seamlessly in an HTML environment (option in configuration file). All the examples are provided both as SVG standalone and embedded in HTML, and are strictly equal.
Besides its universal Node Helper (http://www.svgmagazine.com/jul2011/dom-helper.html) Pergola also provides the equivalent for building HTML nodes and <foreignObject> HTML nodes.
Pro SVG native
The first and most accomplished SVG native library, 100% cross-platform compatible.
Pro Good documentation
Very handy with examples and explanations.
Pro Excellent browser support
Highcharts supports all modern browsers (including IE6 and up), iOS and Android.
Pro Lots of good examples
The site has a selection of good examples that will help you get started quickly.
Pro Supports multiple Y axes
Important for trend correlation, eg. comparing number of clicks to sale amounts. Not same scales / units.
Pro Library to support Microsoft .NET
Compatable with .NET framework 4+, can develop graphs from server side for ASP .NETand ASP .NET MVC applications.
Con Commercial license
PERGOLA does not offer a free version. The price for a single developer to use PERGOLA is 400 €.
Highcharts is not free for commercial projects, with a starting price of US$590 for Single Developer + Maintenance & Support
Con The examples are not that great
For instance, example's JsFiddle may get stalled when loading.