[BioC] ggbio
Xin Yang
xin.yang at cimr.cam.ac.uk
Tue Jul 24 12:19:07 CEST 2012
Hi Tengfei,
Thanks a lot!
autoplot(BamFile(bamfile), which=genesymbol["IFIH1"],method = "raw")
generated the plot successfully , while
library(Rsamtools)
length(biovizBase:::fetch(BamFile(bamfile), which = genesymbol["IFIH1"]))
yields no plot.
Besides, may I ask whether ggbio can plot gtf file? I saw in the
geom_alignment, you simulated a GRanges object, is there a way to plot
gtf file automatically like autoplot?
I saw in your website homepage: http://tengfei.github.com/ggbio/, there
is a very nice track figure (figure5, see attachment please) and I like
it very much. May I ask how you did it? If you could share the codes, it
would be fantastic!
Many thanks for your help!!!
Xin
On 23/07/12 18:01, Tengfei Yin wrote:
> Hi Xin,
>
> This works on my bamfile samples, it's probably sample dependent,
> could be a bug in the package, would you mind try runing
> autoplot(BamFile(bamfile), which=genesymbol["IFIH1"],method = "raw")
>
> and
>
> library(Rsamtools)
> length(biovizBase:::fetch(BamFile(bamfile), which = genesymbol["IFIH1"]))
>
> to see what happened?
>
> Thanks a lot.
>
> Tengfei
>
>
> On Mon, Jul 23, 2012 at 9:17 AM, Xin Yang <xin.yang at cimr.cam.ac.uk
> <mailto:xin.yang at cimr.cam.ac.uk>> wrote:
>
> Hi Tengfei,
>
> Thanks a lot for your reply.
>
> Here is my session Info():
>
> > sessionInfo()
>
> R version 2.15.0 (2012-03-30)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
>
> [7] LC_PAPER=C LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
>
> [1] BiocInstaller_1.5.12 BSgenome.Hsapiens.UCSC.hg19_1.3.17
>
> [3] BSgenome_1.25.3 Rsamtools_1.9.24
>
> [5] Biostrings_2.25.8 GenomicRanges_1.9.39
>
> [7] IRanges_1.15.24 BiocGenerics_0.3.0
>
> [9] ggbio_1.5.10 ggplot2_0.9.1
>
> loaded via a namespace (and not attached):
>
> [1] AnnotationDbi_1.19.28 Biobase_2.17.6 biomaRt_2.13.1
>
> [4] biovizBase_1.5.6 bitops_1.0-4.1 cluster_1.14.2
>
> [7] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4
>
> [10] digest_0.5.2 GenomicFeatures_1.9.28 grid_2.15.0
>
> [13] gridExtra_0.9 Hmisc_3.9-3 labeling_0.1
>
> [16] lattice_0.20-6 MASS_7.3-18 Matrix_1.0-6
>
> [19] memoise_0.1 munsell_0.3 plyr_1.7.1
>
> [22] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1
>
> [25] reshape2_1.2.1 RSQLite_0.11.1 rtracklayer_1.17.13
>
> [28] scales_0.2.1 snpStats_1.7.3 splines_2.15.0
>
> [31] stats4_2.15.0 stringr_0.6 survival_2.36-14
>
> [34] tcltk_2.15.0 tools_2.15.0 VariantAnnotation_1.3.16
>
> [37] XML_3.9-4 zlibbioc_1.3.0
>
> When I installed the package, actually there were some warnings
> that might matter...?
>
> >useDevel(TRUE)
>
> > source("http://bioconductor.org/biocLite.R" <http://bioconductor.org/biocLite.R>)
>
> > biocLite("ggbio")
>
> BioC_mirror:http://bioconductor.org
>
> Using R version 2.15, BiocInstaller version 1.5.12.
>
> Installing package(s) 'ggbio'
>
> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/ggbio_1.5.10.tar.gz'
>
> Content type 'application/x-gzip' length 5820717 bytes (5.6 Mb)
>
> opened URL
>
> ==================================================
>
> downloaded 5.6 Mb
>
> * installing *source* package ‘ggbio’ ...
>
> ** R
>
> ** inst
>
> ** preparing package for lazy loading
>
> Warning: No function found corresponding to methods exports from ‘GenomicFeatures’ for: ‘seqnameStyle’
>
> Warning: found methods to import for function ‘append’ but not the generic itself
>
> Warning: found methods to import for function ‘IQR’ but not the generic itself
>
> Warning: found methods to import for function ‘as.table’ but not the generic itself
>
> Creating a new generic function for ‘rescale’ in package ‘ggbio’
>
> Creating a generic function for ‘summary’ from package ‘base’ in package ‘ggbio’
>
> Creating a generic function for ‘print’ from package ‘base’ in package ‘ggbio’
>
> Creating a new generic function for ‘xlim’ in package ‘ggbio’
>
> Creating a generic function for ‘update’ from package ‘stats’ in package ‘ggbio’
>
> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’
>
> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’
>
> Creating a new generic function for ‘geom_bar’ in package ‘ggbio’
>
> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’
>
> Creating a new generic function for ‘stat_bin’ in package ‘ggbio’
>
> Warning in FUN(X[[1L]], ...) :
>
> Created a package name, ‘2012-07-23 17:11:45’, when none found
>
> ** help
>
> *** installing help indices
>
> ** building package indices
>
> ** installing vignettes
>
> ‘Manhattan.Rnw’
>
> ‘autoplot.Rnw’
>
> ‘chip-seq.Rnw’
>
> ‘circular.Rnw’
>
> ‘ideogram.Rnw’
>
> ‘intro.Rnw’
>
> ‘karyogram.Rnw’
>
> ‘mismatch.Rnw’
>
> ‘rangeslinkedtodata.Rnw’
>
> ‘tracks.Rnw’
>
> ‘txdb.Rnw’
>
> ** testing if installed package can be loaded
>
> Warning: No function found corresponding to methods exports from ‘GenomicFeatures’ for: ‘seqnameStyle’
>
> Warning: found methods to import for function ‘as.list’ but not the generic itself
>
> Warning: found methods to import for function ‘aggregate’ but not the generic itself
>
> Warning: found methods to import for function ‘as.table’ but not the generic itself
>
> Warning: found methods to import for function ‘complete.cases’ but not the generic itself
>
> Warning: found methods to import for function ‘cor’ but not the generic itself
>
> Warning: found methods to import for function ‘append’ but not the generic itself
>
> Warning: found methods to import for function ‘as.data.frame’ but not the generic itself
>
> Warning: found methods to import for function ‘as.list’ but not the generic itself
>
> * DONE (ggbio)
>
> The downloaded source packages are in
>
> ‘/tmp/RtmpLWEw0M/downloaded_packages’
>
> Warning message:
>
> installed directory not writeable, cannot offer to update old packages 'boot',
>
> 'class', 'KernSmooth', 'MASS', 'mgcv', 'nnet', 'rpart', 'spatial'
>
> And the problem is still there.
>
> Many thanks,
> Xin
>
>
> On 23/07/12 16:28, Tengfei Yin wrote:
>> Hi Xin,
>>
>> Could you please sent me your sessionInfo().
>>
>> btw: You can try to install the dev-version of ggbio(by running
>> 'useDevel(TRUE)' in R 2.15 and update ggbio), to see if your
>> problem has been fixed or not.
>>
>> Thanks a lot.
>>
>> Tengfei
>>
>>
>>
>> On Mon, Jul 23, 2012 at 6:35 AM, Xin Yang
>> <xin.yang at cimr.cam.ac.uk <mailto:xin.yang at cimr.cam.ac.uk>> wrote:
>>
>> Dear members,
>>
>> I'm using ggbio to get some coverage plot for bam files and I
>> did:
>>
>> autoplot(bamfile, which=genesymbol["IFIH1"],method = "raw")
>>
>>
>> reading in as Bamfile
>>
>> Error in .local(data, ...) : method 'raw' require which argument
>>
>>
>> It seems the "which" argument doesn't work and I checked the
>> "genesymbol["IFIH1"]" as follows:
>>
>> genesymbol["IFIH1"]
>>
>>
>> GRanges with 1 range and 2 elementMetadata cols:
>>
>> seqnames ranges strand | symbol
>> ensembl_id
>>
>> <Rle> <IRanges> <Rle> |<character> <character>
>>
>> IFIH1 chr2 [163123590, 163175039] - | IFIH1
>> ENSG00000115267
>>
>> ---
>>
>> seqlengths:
>>
>> chr1 chr10 ...
>> chrY
>>
>> NA NA ...
>> NA
>>
>> class(genesymbol["IFIH1"])
>>
>>
>> [1] "GRanges"
>>
>> attr(,"package")
>>
>> [1] "GenomicRanges"
>>
>>
>> Does anyone have a solution?
>> Many thanks,
>>
>> Xin
>>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>> Tengfei Yin
>> MCDB PhD student
>> 1620 Howe Hall, 2274,
>> Iowa State University
>> Ames, IA,50011-2274
>> Homepage: www.tengfei.name <http://www.tengfei.name>
>>
>>
>
>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
> Homepage: www.tengfei.name <http://www.tengfei.name>
>
>
--
Xin Yang
JDRF/WT Diabetes and Inflammation Laboratory
NIHR Cambridge Biomedical Research Centre
Cambridge Institute for Medical Research, University of Cambridge
Wellcome Trust/MRC Building, Addenbrooke's Hospital, Cambridge, CB2 0XY
Tel: 44 (0)1223 763222
Email: xy249 at cam.ac.uk
Website: http://www-gene.cimr.cam.ac.uk/
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