CummeRbund (csVolcano plot) question

[prios]

Hello community,

I’m analyzing the results from an RNA-seq and I’m trying to use CummeRbund to visualize the output from cuffdiff. I’ve got it working all right but my question is:

When using csVolcano plot, is it possible to change the way it shows the significant dots in the plot? Instead of being red-coloured dots, I’d like them to turn into crosses or empty circles to differenciate them with a b&w printer.

I’ve being digging the cummerbund and ggplot manuals but I’ve not being able to do it so I'd be thankful if someone has any suggestion.

Thanks!
Pablo

[AgaricX]

I'd also like to know how to change the graphical output. Point size, color... those parameters would be helpful for creating figures for my upcoming publication.

Thanks in advance,
-Brian

[sepulveda]

HI, I also want to get help on change the graphical output, Point size, color. Anyone?

[glados]

Same here. For the scatter plots and some other plots the code:

+ geom_point(aes(scale_size=2, scale_shape=19))

works great to add to the plot in order to change point size, etc.

But that does not work at all for csVolcano() plot. It looks the same whatever I try..

[glados]

I also want to change the replicate names in cummeRbund, since it gives them own replicate names with numbers from 0 and up. I've tried this:

replicates(cuff)$rep_name <- c("name1","name2","name3")

but it doesn't work. Anyone have any idea? I've spent too much time on things like this in cummeRbund now.

[sepulveda]

Hi, Thanks Glados. I agree with you. Cummerbund is great tool, but it is just too hard to adjust the graph parameters. A lot of time spent. I think the manual should include more details and command line examples.