cummeRbund / ggplot2

[seqfast]

Thank you Loyal and team for cummeRbund, it's a great way to get a good feel for cuffdiff data and perform some nice analyses.

i'm having a little bit of a hard time adjusting certain aspects of the plots, which i believe based on the documentation should be possible as they are all ggplot2 objects. i am not an expert in R, so my questions might be naive.

given a scatter plot (as a matrix) from:

scatterM <- csScatterMatrix(genes(cuff))
scatterM

I would like to adjust what in ggplot2 is alpha, or transparency; i'd like to leave the density plot portion the same (where same conditions are compared).

i've tried a few ggplot2 things, but no luck. i've used ggplot2 in the past with success, but not here, e.g.

scatterM + (geom_point(alpha=1/20))
Error: geom_point requires the following missing aesthetics: x, y

thanks!

-sf

[griffon42]

Any progress?

Has anyone figured this out? I'm struggling as well. In ggplot2, it seems like the issue is an inability to change the "default" layer of the plot, on account of the "data" being fed from the method, rather than a standard, named data frame.

It would be great to get a solution to this.

Thanks.

[krespim]

I am not sure if I understood your question correctly, but have you tried to change the theme of the ggplot session?
http://sape.inf.usi.ch/quick-reference/ggplot2/themes

It should, in principle, set all the visual properties (or change) in a particular session, that is for all the plots generated after the theme is set. My guess is that overrides the cummeRbund call but I am not sure.

[TPH]

Hi,
I am getting same kind of an error while trying to execute following command.
csVolcanoMatrix(genes(cuff_data))

Error: geom_vline requires the following missing aesthetics: xintercept

I tried changing ggplot theme, but it didn't work.
Could anyone please help?

TPH

[AmitChaurasia]

Hi here I am getting same error.

geom_vline requires the following missing aesthetics: xintercept

could anyone help... since I tried all aspects of installing reinstalling the things.

Thanks,

Hi,
I am getting same kind of an error while trying to execute following command.
csVolcanoMatrix(genes(cuff_data))

Error: geom_vline requires the following missing aesthetics: xintercept

I tried changing ggplot theme, but it didn't work.
Could anyone please help?

TPH

[Thias]

I unfortunately can't give you a ready-to-use solution, because I never worked with cummeRbund, but I have quite some experience with the underlying ggplot2 and can shed some light on the error message itself.

aesthetics in ggplot2 are something completely different than the theme. A theme defines the plot's appearence (font sizes, background color, spacing and such), the aesthetics define which data is represented in what way: What is shown on the x-axis, the y-axis and are there categorical variables represented as different colors, sizes, shapes of the dots or patterns of the lines and such.

In your case, geom_vline() is a function to draw a vertical line in the plot, however it lacks the information where this line should be drawn (intersect the x-axis). I guess that is supposed to appear at the median FPKM value or such and that this computation fails, so you have to provide this value manually via the pass-through argument mapping.

csVolcanoMatrix(cuffdata,mapping=aes(xintercept=2))

Also make sure that you provide the correct data type. The function requests objects of the classes CuffData, CuffFeatureSet, or CuffGeneSet. You can check that with the class function

class(cuffdata)
class(genes(cuffdata))

I don't know that the genes() function is and from which package, but it might e.g. return a data.frame, which is no longer suitable.

Hope that helps a bit...

[AmitChaurasia]

Thank You Thias... I hope this should work. I believe that this could be an issue for different version of R.

Best,
Amit