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Question: Gviz Sashimi Plots
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gravatar for edco84
2.5 years ago by
edco840
Buffalo, NY/Roswell Park Cancer Institute
edco840 wrote:

I am trying to do some sashimi plots using directly a bam file obtained from TopHat, I but keep getting the same error message related to the length of the x and y vectors when attempting to do an internal spline routine. I'm sure that my bam file has some junctions in the window of interest and contains cigar strings.

I am able to reproduce the sashimi plot example shown in the Gviz user guide; so I know there is no internal problem in my Gviz version:

library(Gviz) ## Gviz_1.14.4

afrom<-2960000
ato<-3160000
alTrack <- AlignmentsTrack(system.file(package = "Gviz","extdata","gapped.bam"),
                           isPaired =T,
                           chromosome="chr12",
                           genome="hg19")
plotTracks(alTrack,
           from = afrom, to = ato,
           chromosome = "chr12", type=c("coverage","sashimi"))

Now I do the same thing with my bam:

options(ucscChromosomeNames=FALSE) ## Change to my chr nomenclature

mybam11 <- '~/Projects/rMATS_test/data/Dingxiao/BAM/SRR923927.bam'
aliTrack11 <- AlignmentsTrack(mybam11, chromosome=21, genome='hg19') 

augr <- gex[gex$gene_id=='NDUFV3', ] ## My annotation in a GRanges object

augr <- GRanges(seqnames=seqnames(augr),
                ranges=IRanges(start(augr), end(augr)))

myTrans <- AnnotationTrack(range=augr,
                           genome='hg19',
                           name='NDUFV3')

pdf('sashimi1.pdf')
plotTracks(aliTrack11,
           from=min(start(augr)), to=max(end(augr)),
           type=c('coverage', 'sashimi'))
dev.off()

Error in validDetails.xspline(x) : 'x' and 'y' must be same length
> null device 
          1 

I am wondering if there is something wrong with my bam file or how Gviz is reading it.

> sessionInfo()
R version 3.2.4 Revised (2016-03-16 r70336)
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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
[1] Gviz_1.14.4          GenomicRanges_1.22.4 GenomeInfoDb_1.6.3  
[4] IRanges_2.4.8        S4Vectors_0.8.11     BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3                compiler_3.2.4            
 [3] RColorBrewer_1.1-2         futile.logger_1.4.1       
 [5] plyr_1.8.3                 XVector_0.10.0            
 [7] GenomicFeatures_1.22.13    bitops_1.0-6              
 [9] futile.options_1.0.0       tools_3.2.4               
[11] zlibbioc_1.16.0            rpart_4.1-10              
[13] biomaRt_2.26.1             digest_0.6.9              
[15] BSgenome_1.38.0            gtable_0.2.0              
[17] RSQLite_1.0.0              lattice_0.20-33           
[19] biovizBase_1.18.0          DBI_0.3.1                 
[21] gridExtra_2.2.1            cluster_2.0.3             
[23] rtracklayer_1.30.3         Biostrings_2.38.4         
[25] nnet_7.3-12                Biobase_2.30.0            
[27] AnnotationDbi_1.32.3       XML_3.98-1.4              
[29] survival_2.38-3            BiocParallel_1.4.3        
[31] foreign_0.8-66             Formula_1.2-1             
[33] latticeExtra_0.6-28        ggplot2_2.1.0             
[35] lambda.r_1.1.7             Rsamtools_1.22.0          
[37] scales_0.4.0               Hmisc_3.17-2              
[39] matrixStats_0.50.1         GenomicAlignments_1.6.3   
[41] splines_3.2.4              dichromat_2.0-0           
[43] SummarizedExperiment_1.0.2 colorspace_1.2-6          
[45] acepack_1.3-3.3            RCurl_1.95-4.8            
[47] munsell_0.4.3              VariantAnnotation_1.16.4

Thank you for your attention,

EC

ADD COMMENTlink modified 2.5 years ago by Robert Ivanek530 • written 2.5 years ago by edco840
2
gravatar for Robert Ivanek
2.5 years ago by
Robert Ivanek530
Switzerland
Robert Ivanek530 wrote:

Thanks Eduardo for reporting this bug. I have just uploaded fixed code to the SVN (release 1.14.5,  devel 1.15.5).

ADD COMMENTlink written 2.5 years ago by Robert Ivanek530
0
gravatar for Robert Ivanek
2.5 years ago by
Robert Ivanek530
Switzerland
Robert Ivanek530 wrote:

Could you share with me the BAM file (or rather its subset with the region of interest)?

Robert

ADD COMMENTlink written 2.5 years ago by Robert Ivanek530
0
gravatar for edco84
2.5 years ago by
edco840
Buffalo, NY/Roswell Park Cancer Institute
edco840 wrote:

Sure. I hope the link works.

https://www.sugarsync.com/pf/D9723058

 

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by edco840
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