Hello,
After completing all the analysis steps from Tophat to Cudiff, I am trying to plot the data using CummeRbund. But I get this error message saying "semi-transparency is not supported on this device: reported only once per page".
I work in a cluster using Linux and use R/3.2.2 compiled with Cairo. Could you please help me to fugure out the issue here.
These are the commands and their outputs I received.
$ module load R/3.2.2
$ R
>library(cummeRbund)
>cuff_data <‐ readCufflinks('/Path to cuffdiff output folder/cuffdiff_out')
>csDensity(genes(cuff_data))
Removed 8804 rows containing non-finite values (stat_density).
2: In grid.Call.graphics(L_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
---------------------------------------------------------------
I feel like there is an issue with the cummeRbund loading. But I can't figure out what is it. This is the output I get when cummeRbund Loads.
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘packagearallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: ‘cummeRbund’
The following object is masked from ‘package:GenomicRanges’:
promoters
The following object is masked from ‘package:IRanges’:
promoters
The following object is masked from ‘package:BiocGenerics’:
Conditions
Could you please help.
Thank you very much.
TPH
After completing all the analysis steps from Tophat to Cudiff, I am trying to plot the data using CummeRbund. But I get this error message saying "semi-transparency is not supported on this device: reported only once per page".
I work in a cluster using Linux and use R/3.2.2 compiled with Cairo. Could you please help me to fugure out the issue here.
These are the commands and their outputs I received.
$ module load R/3.2.2
$ R
>library(cummeRbund)
>cuff_data <‐ readCufflinks('/Path to cuffdiff output folder/cuffdiff_out')
>csDensity(genes(cuff_data))
Removed 8804 rows containing non-finite values (stat_density).
2: In grid.Call.graphics(L_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
---------------------------------------------------------------
I feel like there is an issue with the cummeRbund loading. But I can't figure out what is it. This is the output I get when cummeRbund Loads.
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘packagearallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist, unsplit
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: ‘cummeRbund’
The following object is masked from ‘package:GenomicRanges’:
promoters
The following object is masked from ‘package:IRanges’:
promoters
The following object is masked from ‘package:BiocGenerics’:
Conditions
Could you please help.
Thank you very much.
TPH