Question

remove background color from dba.plotVolcano (Diffbind)

0

Entering edit mode

hy • 0

@hy-23158

Last seen 4.7 years ago

Hello,

Maybe it's a simple question, but I would like to remove the background color (gray shade) from the volcano plot of Diffbind result :

dba.plotVolcano(db)

Any comments or suggestions would be greatly appreciated. Thank you.

diffbind • 1.2k views

ADD COMMENT • link updated 4.7 years ago by James W. MacDonald 67k • written 4.7 years ago by hy • 0

score 1 · Answer 1 · 2020-03-23

1

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days ago

United States

It's generated using ggplot2, so you can just change the theme

dba.plotVolcano(db) + theme_bw()

If you care to know more about that sort of thing, you need to read up on ggplot2, rather than DiffBind.

ADD COMMENT • link 4.7 years ago James W. MacDonald 67k

0

Entering edit mode

Thanks a lot for the comment and suggestion, James. But this script doesn't seem to work for me. It gave "NULL" message without changing the graph. I also read about ggplot2 and tried theme_bw(), and it works well with ggplot().

But it doesn't change the themes with dba.plotVolcano()

> dba.plotVolcano(db) + theme_bw()
NULL

I don't know if there's something that I missed..

ADD REPLY • link 4.7 years ago hy • 0

0

Entering edit mode

OK, so that's sort of different. What dba.plotVolcano does is

Make a volcano plot
If requested, return something completely different (a GRanges object)

Which isn't what I would normally expect in that situation. The quick hack is to do

debug(DiffBind:::pv.DBAplotVolcano)
dba.plotVolcano(db)
## keep hitting enter until you get to 
plot(p)
## and then do
p + theme_bw()