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
