Sorry, I couldn't find a simple way of connecting two values using a bar type chart/graph : the "fill base line to plot n" function is not available for bar plots.
I may miss something here, but, if as you said, you may have hundreds of points, a bar plot would be of very little interest, and a curve plot could also do the trick.
A possible solution could be to divide the data into 2 differents sets : one when Y1>= Y2, the other when Y2>Y1, and to plot the 4 arrays as curves, using the "fill base line" function to distinguish the 2 sets, as in the attached vi.
This does not work as it with bar plots, since bars are always filled to zero. The only way of approching a solution would be to plot the smaller set as BLACK bars OVER the larger set, if they have the same sign, or in the same color otherwise. Accordingly, a more complicated work around, that answers more closely your question, would be to create 4 differents sets, the 2 previous sets being divided in 2 subsets, depending on the relative sign of the Y values. One drawback however, is that the grid lines would be hidden by the black bars...
Hope this helps.
CC
Chilly Charly (aka CC)
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