Question: Error in `rownames : Gviz plotTracks
1
gravatar for gpwhiz
10 months ago by
gpwhiz10
gpwhiz10 wrote:

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.

ADD COMMENTlink written 10 months ago by gpwhiz10

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

 

ADD REPLYlink written 10 months ago by Robert Ivanek650

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!!

ADD REPLYlink written 10 months ago by gpwhiz10

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))
ADD REPLYlink modified 10 months ago • written 10 months ago by gpwhiz10

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

ADD REPLYlink written 10 months ago by Robert Ivanek650
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