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When a chart as negative values, the tooltips are not well displayed. It's like negative values add a sort of padding.
You can see examples here : http://eunomie.github.io/flot.tooltip.bug. On each page there's two set of datas. One starting with negative values, one only with positive values.
In the first page, if you hover negative values, no tooltip is displayed. And the tooltip over the first positive values displayed negative values.
The second page contains same datas but use a patched version of flot.tooltip which use
item.datapoint
instead ofitem.series.data[item.dataIndex]
to access datas of the point. And with this modification all tooltips are well displayed.