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Old 01-21-2013, 08:18 AM   #1
prios
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Default CummeRbund (csVolcano plot) question

Hello community,

Iím analyzing the results from an RNA-seq and Iím trying to use CummeRbund to visualize the output from cuffdiff. Iíve 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, Iíd like them to turn into crosses or empty circles to differenciate them with a b&w printer.

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

Thanks!
Pablo
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Old 02-08-2013, 03:45 PM   #2
AgaricX
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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
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Old 06-12-2013, 10:19 AM   #3
sepulveda
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HI, I also want to get help on change the graphical output, Point size, color. Anyone?
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Old 07-01-2013, 06:51 AM   #4
glados
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Same here. For the scatter plots and some other plots the code:
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..
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Old 07-01-2013, 07:00 AM   #5
glados
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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:

Code:
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.
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Old 07-01-2013, 03:22 PM   #6
sepulveda
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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.
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cummerbund 2, cummerbund plots, rna-seq, volcano plot

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