Not really, no. What you can do is specify how wide / high the axis marks should be, which make the canvas align between different graphs.
From API.txt :
"labelWidth" and "labelHeight" indicate a fixed tick tick size in pixels. They are useful if you need to align several sections. "reserveSpace" means that even if the axis is not shown, Flot must reserve a place for it - it is useful in combination with labelWidth and labelHeight to align multi-axis diagrams.
In addition, if you want the actual axes to be the same between the graphs, you will need to set which global min / max for each axis between all your datasets, and then indicate what for each axis on each graph.
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