Error in `rownames : Gviz plotTracks
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gpwhiz ▴ 10
@gpwhiz-19034
Last seen 5.3 years ago

Hello,

I am getting the following errors when using plotTracks in Gviz. here, I am just following examples provided in the vignette https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf

for plotting Annotation track, I used the following code

> data("cpgIslands")
> atrack <- AnnotationTrack(cpgIslands,name="CpG")
> plotTracks(atrack)
Error in `rownames<-`(`*tmp*`, value = c("1", "10", "2", "3", "4", "5",  : 
  invalid rownames length

I also tried using the GeneRegiontrack and I again I get an error when executing the plotTracks about rownames

> data(geneModels)
> gen <- genome(cpgIslands)
> chr <- as.character(unique(seqnames(cpgIslands)))
> grtrack <- GeneRegionTrack(geneModels, genome=gen,chromosome=chr, name="Gene Model")
> plotTracks(grtrack)
Error in `rownames<-`(`*tmp*`, value = c("ENST00000242109", "ENST00000345317",  : 
  invalid rownames length

I am following the directions from the tutorials, so I am confused as to what mistake i am making here.

Any advice is much appreciated.

gviz plottracks generegiontrack • 1.3k views
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Hi,

I have just checked the code in both release and level versions and it worked for me. Could you please your sessionInfo? 

Best, Robert

 

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Hi Robert!

Thank you for your prompt response.

This is my Sessioninfo

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] Gviz_1.26.4                             biovizBase_1.30.1                      
 [3] ggbio_1.30.0                            ggplot2_3.1.0                          
 [5] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] org.Hs.eg.db_3.6.0                      GO.db_3.6.0                            
 [9] OrganismDbi_1.24.0                      GenomicFeatures_1.32.2                 
[11] AnnotationDbi_1.42.1                    Biobase_2.40.0                         
[13] GenomicRanges_1.32.6                    GenomeInfoDb_1.16.0                    
[15] IRanges_2.14.10                         S4Vectors_0.20.1                       
[17] BiocGenerics_0.28.0                    

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.14.0         bitops_1.0-6                matrixStats_0.54.0         
 [4] bit64_0.9-7                 RColorBrewer_1.1-2          progress_1.2.0             
 [7] httr_1.4.0                  tools_3.5.1                 backports_1.1.3            
[10] R6_2.3.0                    rpart_4.1-13                Hmisc_4.1-1                
[13] DBI_1.0.0                   lazyeval_0.2.1              colorspace_1.3-2           
[16] nnet_7.3-12                 withr_2.1.2                 gridExtra_2.3              
[19] prettyunits_1.0.2           GGally_1.4.0                curl_3.2                   
[22] bit_1.1-14                  compiler_3.5.1              graph_1.60.0               
[25] htmlTable_1.12              DelayedArray_0.8.0          rtracklayer_1.40.5         
[28] scales_1.0.0                checkmate_1.8.5             RBGL_1.58.1                
[31] stringr_1.3.1               digest_0.6.18               Rsamtools_1.34.0           
[34] foreign_0.8-70              XVector_0.20.0              dichromat_2.0-0            
[37] base64enc_0.1-3             pkgconfig_2.0.2             htmltools_0.3.6            
[40] ensembldb_2.4.1             BSgenome_1.50.0             htmlwidgets_1.3            
[43] rlang_0.3.0.1               rstudioapi_0.8              RSQLite_2.1.1              
[46] BiocInstaller_1.32.1        BiocParallel_1.16.2         acepack_1.4.1              
[49] VariantAnnotation_1.28.3    RCurl_1.95-4.11             magrittr_1.5               
[52] GenomeInfoDbData_1.2.0      Formula_1.2-3               Matrix_1.2-14              
[55] Rcpp_1.0.0                  munsell_0.5.0               stringi_1.2.4              
[58] yaml_2.2.0                  SummarizedExperiment_1.12.0 zlibbioc_1.28.0            
[61] plyr_1.8.4                  blob_1.1.1                  crayon_1.3.4               
[64] lattice_0.20-35             Biostrings_2.50.1           splines_3.5.1              
[67] hms_0.4.2                   knitr_1.21                  pillar_1.3.1               
[70] reshape2_1.4.3              biomaRt_2.38.0              XML_3.98-1.16              
[73] latticeExtra_0.6-28         data.table_1.11.8           BiocManager_1.30.4         
[76] gtable_0.2.0                reshape_0.8.8               assertthat_0.2.0           
[79] xfun_0.4                    AnnotationFilter_1.4.0      survival_2.42-3            
[82] tibble_1.4.2                GenomicAlignments_1.18.0    memoise_1.1.0              
[85] cluster_2.0.7-1  

 

Thank you so much for helping me!!

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Hi,

I also tried the traceback, but I don't understand the problem

plotTracks(list(gtrack,atrack))
Error in `rownames<-`(`*tmp*`, value = c("1", "10", "2", "3", "4", "5",  : 
  invalid rownames length
>  traceback()
27: stop("invalid rownames length")
26: `rownames<-`(`*tmp*`, value = c("1", "10", "2", "3", "4", "5", 
    "6", "7", "8", "9"))
25: `rownames<-`(`*tmp*`, value = c("1", "10", "2", "3", "4", "5", 
    "6", "7", "8", "9"))
24: .local(x, use.names, ...)
23: elementMetadata(x, use.names = use.names, ...)
22: elementMetadata(x, use.names = use.names, ...)
21: mcols(x)
20: mcols(x)
19: .reconcileMetadatacols(ans)
18: newCompressedList0(ans_class, flesh, skeleton)
17: relist(x, f)
16: relist(x, f)
15: .splitAsList_by_factor(x, f, drop)
14: splitAsList_default(x, f, drop = drop)
13: .local(x, f, drop, ...)
12: IRanges::splitAsList(x, f, drop = drop)
11: IRanges::splitAsList(x, f, drop = drop)
10: .local(x, f, drop, ...)
9: split(ranges(x), group(x))
8: split(ranges(x), group(x))
7: unlist(range(split(ranges(x), group(x))))
6: .local(x, ...)
5: FUN(X[[i]], ...)
4: FUN(X[[i]], ...)
3: lapply(trackList, subset, from = ranges["from"], to = ranges["to"], 
       chromosome = chromosome)
2: lapply(trackList, subset, from = ranges["from"], to = ranges["to"], 
       chromosome = chromosome)
1: plotTracks(list(gtrack, atrack))
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Entering edit mode

I have just checked your sessionInfo and realised that you have a picture of packages from current release and some older ones, for example: GenomicRanges, GenomicFeatures, Biobase and few others. Can you please update your packages and try again? 

Best

Robert

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