[BioC] DiffBind

Rory Stark Rory.Stark at cruk.cam.ac.uk
Tue Apr 1 18:37:29 CEST 2014

Hello Igor-

This feature has just been added to the upcoming release of DiffBind. It
is part of Bioconductor 2.14, due to be released 14 April, and currently
available in the Development branch.

dba.plotPCA has been reworked to use xyplot() from the lattice package. It
now automatically draws a legend alongside the plot, and there is a new
parameter, labels, for labelling the points on the plot. So a call of the

> dba.plotPCA(DBA,attributes=DBA_CONDITION,labels=DBA_ID)

Will color the points according to the Condition metadata field, and label
each of them using the sample Id string. If you aren't yet using the
developer version, you can see what the new plots look like (the colors
have been changed to be a bit more pleasant as well) by looking at the
latest version of the vignette:


with labelled examples on pages 10, 11, and 17.

On 01/04/2014 01:31, "Dolgalev, Igor" <Igor.Dolgalev at nyumc.org> wrote:

>Sorry to bother you. I am trying out DiffBind package that you maintain.
>I am very happy with it. The only problem I have is with the plotPCA
>function. I can¹t seem to figure out how to add the right parameter to
>have the points labeled with sample names. Is that possible? For
>plotHeatmap, it was easy to modify the default behavior (it¹s just
>calling heatmap.2), but plotPCA seems to be a lot trickier.
>Thank you very much.
>This email message, including any attachments, is for t...{{dropped:13}}

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