The best open source alternative to Highcharts is D3.js, which is both free and Open Source. If that doesn't suit you, our users have ranked more than 25 alternatives to Highcharts and many of them is open source so hopefully you can find a suitable replacement. Other interesting open source alternatives to Highcharts are RAWGraphs (Free, Open Source), Plotly (Freemium, Open Source), Bokeh (Free, Open Source) and NVD3 (Free, Open Source).
D3 allows you to bind arbitrary data to a Document Object Model (DOM), and then apply data-driven transformations to the document. For example, you can use D3 to generate an HTML table from an array of numbers.
RAWGraphs is an open source app built with the goal of making the visualization of complex data easy for everyone. Born as tool for designers and vis geeks, RAWGraphs aims at providing a missing link between spreadsheets and vector graphics editors.
vis.js is a dynamic, browser based visualization library. The library is designed to be easy to use, to handle large amounts of dynamic data, and to enable manipulation of and interaction with the data.