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Question: A bug when plotting Gviz data
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gravatar for dustar1986
10 weeks ago by
dustar19860
dustar19860 wrote:

Hi,

I found an interesting BUG in Gviz v1.20. I have a data frame `new` for transcripts, each line is an exon. Column names are `chromosome`, `start`, `end`, `width`, `strand`, `feature`, `gene`, `exon`, `transcript`, `symbol` and `color`. The information in `gene`, `transcript` and `symbol` are identical. 

I called the function:

 

newtrack <- GeneRegionTrack(new)

gtrack <- GenomeAxisTrack()

plotTracks(list(gtrack,newtrack),stackHeight=0.3)

 

Some exons and transcripts are messed up. I found that is one gene name start with letter `c` which leads to the failure. If I renamed it, everything works. I also confirmed change any gene/transcript name to one starting with `c` will reproduce the error. 

I'm wondering where the bug comes from. And here is my R session information:

 

Best,

Dadi

 

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

attached base packages:
character(0)

other attached packages:
[1] Gviz_1.20.0

loaded via a namespace (and not attached):
 [1] Biobase_2.36.2                httr_1.3.1                    bit64_0.9-7                   AnnotationHub_2.8.2           splines_3.4.1                
 [6] shiny_1.0.5                   Formula_1.2-2                 interactiveDisplayBase_1.14.0 stats4_3.4.1                  latticeExtra_0.6-28          
[11] grDevices_3.4.1               blob_1.1.0                    BSgenome_1.44.1               GenomeInfoDbData_0.99.0       Rsamtools_1.28.0             
[16] yaml_2.1.14                   RSQLite_2.0                   backports_1.1.0               lattice_0.20-35               biovizBase_1.24.0            
[21] base_3.4.1                    digest_0.6.12                 GenomicRanges_1.28.5          RColorBrewer_1.1-2            XVector_0.16.0               
[26] checkmate_1.8.3               colorspace_1.3-2              httpuv_1.3.5                  htmltools_0.3.6               Matrix_1.2-11                
[31] plyr_1.8.4                    XML_3.98-1.9                  biomaRt_2.32.1                zlibbioc_1.22.0               xtable_1.8-2                 
[36] scales_0.5.0                  BiocParallel_1.10.1           htmlTable_1.9                 tibble_1.3.4                  datasets_3.4.1               
[41] AnnotationFilter_1.0.0        IRanges_2.10.3                ggplot2_2.2.1                 SummarizedExperiment_1.6.3    GenomicFeatures_1.28.4       
[46] nnet_7.3-12                   BiocGenerics_0.22.0           lazyeval_0.2.0                mime_0.5                      survival_2.41-3              
[51] magrittr_1.5                  memoise_1.1.0                 methods_3.4.1                 foreign_0.8-69                utils_3.4.1                  
[56] BiocInstaller_1.26.1          tools_3.4.1                   data.table_1.10.4             matrixStats_0.52.2            stringr_1.2.0                
[61] S4Vectors_0.14.4              munsell_0.4.3                 cluster_2.0.6                 DelayedArray_0.2.7            AnnotationDbi_1.38.2         
[66] ensembldb_2.0.4               stats_3.4.1                   Biostrings_2.44.2             compiler_3.4.1                GenomeInfoDb_1.12.2          
[71] rlang_0.1.2                   grid_3.4.1                    RCurl_1.95-4.8                dichromat_2.0-0               VariantAnnotation_1.22.3     
[76] graphics_3.4.1                htmlwidgets_0.9               bitops_1.0-6                  base64enc_0.1-3               gtable_0.2.0                 
[81] curl_2.8.1                    DBI_0.7                       R6_2.2.2                      GenomicAlignments_1.12.2      gridExtra_2.3                
[86] knitr_1.17                    rtracklayer_1.36.4            bit_1.1-12                    Hmisc_4.0-3                   ProtGenerics_1.8.0           
[91] stringi_1.1.5                 parallel_3.4.1                Rcpp_0.12.12                  rpart_4.1-11                  acepack_1.4.1

 

ADD COMMENTlink modified 9 weeks ago • written 10 weeks ago by dustar19860
0
gravatar for florian.hahne@novartis.com
10 weeks ago by
Switzerland

Hi Dadi,

could you compile a short reproducible example for me to take a look at? Also pointing out what exactly gets messed up?

Thanks,

Florian

ADD COMMENTlink written 10 weeks ago by florian.hahne@novartis.com1.5k
0
gravatar for dustar1986
9 weeks ago by
dustar19860
dustar19860 wrote:

Hi Florian,

Here is a link to my file.

https://drive.google.com/file/d/0B0LC8cC9lS-yeUlBcS1TZjBkcW8/view?usp=sharing

What I used to generate figure is

new = read.table("Input.txt",header=T)
newtrack <- GeneRegionTrack(new)
gtrack <- GenomeAxisTrack()
plotTracks(list(gtrack,newtrack),stackHeight=0.3)

 

This gives me a plot where quite a lot exons are not aligned along their transcript backbones but sit randomly in the panel (most of them are at bottom). If I subsetted my data by excluding the transcript name starting with small letter "c", I can correctly generate the plot. And then, if I renamed any of these transcripts to a new name starting with small letter "c", a similar incorrect figure will be generated. 

I'm wondering if "c" is interpreted as something else in Gviz but I haven't checked "plotTracks" function into details. So not sure if that's caused by Gviz or my R compiling.

 

Thanks in advance.

 

Best,

Dadi

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by dustar19860
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