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Hi all,
I am just running the cummerbund R script and running into a problem when i make the volcano plots. Its only with the volcano plots and other plots look fine, density and scatter. What am i doing wrong? Below is the output...
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> data <-readCufflinks ("all_samples")
Creating database all_samples/cuffData.db
Reading all_samples/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading all_samples/promoters.diff
Writing promoterDiffData table
Reading all_samples/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading all_samples/isoform_exp.diff
Writing isoformExpDiffData table
Reading all_samples/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading all_samples/tss_group_exp.diff
Writing TSSExpDiffData table
Reading all_samples/splicing.diff
Writing splicingDiffData table
Reading all_samples/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading all_samples/cds_exp.diff
Writing CDSExpDiffData table
Reading all_samples/cds.diff
Writing CDSDiffData table
Indexing Tables...
> csDensity(genes(data))
> csScatter(genes(data), 'Infected', 'Uninfected')
> csVolcano(genes(data), 'Infected', 'Uninfected')
Error in if (nrow(layer_data) == 0) return() : argument is of length zero
Also is there a way i can change the X axis of the volcano plots so that they all look similar? When i searched around ...I found the code in another thread..So can i switch the scale_y_continuous to scale_x_continuous? or do i just use xlimits= c(-x, x ).
v<-csVolcano(genes(cuff),'Sample_A','Sample_B')
v+ scale_y_continuous(limits = c(0, 20))
Session info
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cummeRbund_1.2.0 reshape2_1.2.1 ggplot2_0.9.1 RSQLite_0.11.1
[5] DBI_0.2-5
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 grid_2.15.0
[5] labeling_0.1 MASS_7.3-18 memoise_0.1 munsell_0.3
[9] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.1
[13] stringr_0.6 tools_2.15.0
>
I am just running the cummerbund R script and running into a problem when i make the volcano plots. Its only with the volcano plots and other plots look fine, density and scatter. What am i doing wrong? Below is the output...
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> data <-readCufflinks ("all_samples")
Creating database all_samples/cuffData.db
Reading all_samples/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading all_samples/promoters.diff
Writing promoterDiffData table
Reading all_samples/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading all_samples/isoform_exp.diff
Writing isoformExpDiffData table
Reading all_samples/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading all_samples/tss_group_exp.diff
Writing TSSExpDiffData table
Reading all_samples/splicing.diff
Writing splicingDiffData table
Reading all_samples/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading all_samples/cds_exp.diff
Writing CDSExpDiffData table
Reading all_samples/cds.diff
Writing CDSDiffData table
Indexing Tables...
> csDensity(genes(data))
> csScatter(genes(data), 'Infected', 'Uninfected')
> csVolcano(genes(data), 'Infected', 'Uninfected')
Error in if (nrow(layer_data) == 0) return() : argument is of length zero
Also is there a way i can change the X axis of the volcano plots so that they all look similar? When i searched around ...I found the code in another thread..So can i switch the scale_y_continuous to scale_x_continuous? or do i just use xlimits= c(-x, x ).
v<-csVolcano(genes(cuff),'Sample_A','Sample_B')
v+ scale_y_continuous(limits = c(0, 20))
Session info
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cummeRbund_1.2.0 reshape2_1.2.1 ggplot2_0.9.1 RSQLite_0.11.1
[5] DBI_0.2-5
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 grid_2.15.0
[5] labeling_0.1 MASS_7.3-18 memoise_0.1 munsell_0.3
[9] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.1
[13] stringr_0.6 tools_2.15.0
>
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