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Transparent markers

http://undocumentedmatlab.com/blog/plot-markers-transparency-and-color-gradient

Example with ~500,000 points

>> figure, l = plot(x,y,'.')
>> l.MarkerHandle.EdgeColorData(4) = 10

 to 

You'll need to add a listener to change the transparency when the figure is resized, see comments in above thread.

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