DiffBind MA plot
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@grundelphine-14815
Last seen 3.8 years ago

Hi,

I have a small question about the interpretation of the colours assigned to the dots in the MA plots obtained with the DiffBind package:
red dots represent significantly differentially bound sites but what about the dark blue dots, the ones that are close to the borders and sometimes near to the red dots?

Thanks in advance for your help!

Delphine

diffbind maplot • 627 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 19 days ago
CRUK, Cambridge, UK

By default the MA plot is plotted using the smoothScatter function. Instead of every point being plotted, the densities of points at different regions of the plot are indicated using shades of blue. The solid blue dots are an artefact of this smoothing (DiffBind plots the red points over the smoothed plot). So solid blue points are not indicating anything meaningful.

You can see the plot without the smoothing by setting bSmooth=FALSE.

Cheers-

Rory

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thanks for this quick and detailed answer!

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The solid blue dots can be removed by adding smoothScatter parameter nrpoints = 0 like

dba.plotMA(chipdata, nrpoints = 0)

It may be good to make that the default parameter for dba.plotMA.

Vince

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I'll put it on the list!

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