Question: cummeRbund change point size in volcano plot
gravatar for ianmisner17
5.0 years ago by
United States
ianmisner1720 wrote:


I’m working with cummeRbund in R 3.1.1 and I’m trying to get a different point size for my csVolcano plot. I’ve tried two approaches an neither see to work.

after loading library and the data as


cuff <- readCufflinks(“diff_out”)

1)use the mapping setting for the csVoclano function

v <- csVolcano(genes(cuff), “EP”, “PC”, showSignificant=TRUE, alpha=0.05, mapping=aes(size=5))

When I view this the point size stays a the default settings.

2) Alter the ggplot2 information after creating the plot

t <- v + geom_point(aes(size = 2))

This produces an error saying that “geom_point requires the following missing aesthetics: x, y

if I provide those labels the points still don’t change

t <- v + geom_point(aes(x=log10 y=log2 size =2))

Using method two with csScatter works great and the points change size.

What am I missing?


ADD COMMENTlink modified 5.0 years ago by James W. MacDonald51k • written 5.0 years ago by ianmisner1720
Answer: cummeRbund change point size in volcano plot
gravatar for James W. MacDonald
5.0 years ago by
United States
James W. MacDonald51k wrote:

Try this:

v+geom_point(aes(x=log2_fold_change, y = -log10(p_value), color = significant), size=2)
ADD COMMENTlink written 5.0 years ago by James W. MacDonald51k

When I try this I get another error

Error in eval(expr, envir, enclos) : object 'log2_fold_change' not found

if I put the x and y values in quotes I then receive a different error:

Error: Discrete value supplied to continuous scale 
ADD REPLYlink written 4.9 years ago by ianmisner1720
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