Question: Givz sashimi plot controlling the height of plots.
0
gravatar for r.a.lowe1
3.2 years ago by
r.a.lowe10
r.a.lowe10 wrote:

Hi all,

I am trying to plot a sashimi plot for a RNA-seq experiment but whenever I use the sashimi type in Gviz it squashes the output either to PNG or to Quartz.

Any ideas on how to fix?

Updated with code example:

afrom <- 2960000

ato <- 3160000

alTrack <- AlignmentsTrack(system.file(package = "Gviz","extdata", "gapped.bam"), isPaired = TRUE)

bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr12", start = afrom, end = ato, filter = list(with_ox_refseq_mrna = TRUE), stacking = "dense")

plotTracks(c(bmt, alTrack, alTrack), from = afrom + 12700,to = afrom + 15200, chromosome = "chr12", type = c("coverage","sashimi"))

 

Thanks,

Rob


gviz sashimi plots • 802 views
ADD COMMENTlink modified 3.2 years ago by Robert Ivanek590 • written 3.2 years ago by r.a.lowe10

Can you please provide reproducible example of your code and your sessionInfo?

ADD REPLYlink written 3.2 years ago by Robert Ivanek590

 

I have updated the question with reproducible example code.

 

SessionInfo below:

R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] Gviz_1.14.5          GenomicRanges_1.22.4 GenomeInfoDb_1.6.3   IRanges_2.4.8        S4Vectors_0.8.11     BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4                RColorBrewer_1.1-2         futile.logger_1.4.1        plyr_1.8.3                 XVector_0.10.0             GenomicFeatures_1.22.13   
 [7] bitops_1.0-6               futile.options_1.0.0       tools_3.2.4                zlibbioc_1.16.0            rpart_4.1-10               biomaRt_2.26.1            
[13] digest_0.6.9               BSgenome_1.38.0            gtable_0.2.0               RSQLite_1.0.0              lattice_0.20-33            biovizBase_1.18.0         
[19] DBI_0.3.1                  gridExtra_2.2.1            cluster_2.0.3              rtracklayer_1.30.3         Biostrings_2.38.4          nnet_7.3-12               
[25] Biobase_2.30.0             AnnotationDbi_1.32.3       XML_3.98-1.4               survival_2.38-3            BiocParallel_1.4.3         foreign_0.8-66            
[31] Formula_1.2-1              latticeExtra_0.6-28        ggplot2_2.1.0              lambda.r_1.1.7             Rsamtools_1.22.0           scales_0.4.0              
[37] Hmisc_3.17-2               matrixStats_0.50.1         GenomicAlignments_1.6.3    splines_3.2.4              dichromat_2.0-0            SummarizedExperiment_1.0.2
[43] colorspace_1.2-6           acepack_1.3-3.3            RCurl_1.95-4.8             munsell_0.4.3              VariantAnnotation_1.16.4  

ADD REPLYlink written 3.2 years ago by r.a.lowe10
Answer: Givz sashimi plot controlling the height of plots.
1
gravatar for Robert Ivanek
3.2 years ago by
Robert Ivanek590
Switzerland
Robert Ivanek590 wrote:

Dear Rob, thanks for reporting this bug, I fixed the plot layout in both devel and release version (1.14.6, 1.15.6)

ADD COMMENTlink written 3.2 years ago by Robert Ivanek590
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