I have tried to use excellent graph js library http://www.highcharts.com with thingSpeak,
to show multiple graphs from multiple channels.
I am quite happy with it.
result can be seen at http://peter.kmet.sk/okno/
all the code is just js/html please feel free to re-use and modify
possible hints for improvement: live data loading, data interpolation in case point in time is missing
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