Question: diffbind dba.plotvolcano bLabels option use genames instead of numbers
0
gravatar for theodore.georgomanolis
4 months ago by
Germany

Hi all, So am using the diffbind R package and I was doing some plots after analyzing my samples. using the dba.plotVolcano and the option

bLabels = TRUE

I can have the location of those 50 genes that are on the top of the list.

That is great but is not that informative

Is it possible instead of the numbers to plot the gene names?

P.S. is it possible to import the table to another package and plot the volcano plotting function, as described in the following link? https://www.gettinggeneticsdone.com/2016/01/repel-overlapping-text-labels-in-ggplot2.html what do I need to transform or change?

diffbind • 138 views
ADD COMMENTlink modified 12 weeks ago by Rory Stark2.9k • written 4 months ago by theodore.georgomanolis0
Answer: diffbind dba.plotvolcano bLabels option use genames instead of numbers
0
gravatar for Rory Stark
12 weeks ago by
Rory Stark2.9k
CRUK, Cambridge, UK
Rory Stark2.9k wrote:

DiffBind currently does not support adding labels such as gene names to the differentially bound sites.

As you suggest, the best bet is to export the table, and annotate and plot it using other tools. You can get the full table either using dba.report() with th=1, or use only the differentially bound sites by assigning the return value from the call to dba.plotVolcano(). The relevant fields are the FDR and Fold columns in the table.

ADD COMMENTlink written 12 weeks ago by Rory Stark2.9k

Thank you Roy for the answer, do you plan to implement an option as such?

ADD REPLYlink written 11 weeks ago by theodore.georgomanolis0

This is on my list of possible features to add, but there are a number of things ahead of it! The main thing it requires is an interface to add an annotation to the peakset, as most ChIP peak intervals do not correspond directly to annotated genes.

ADD REPLYlink written 11 weeks ago by Rory Stark2.9k

this is true, although the dogma since the GREAT/bedtools days is the closest gene is the relevant one. Although all the looping data do or do not confirm it.

ADD REPLYlink written 10 weeks ago by theodore.georgomanolis0
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