Question: autoplot error {ggbio} when plotting karyogram/ideogram
1
gravatar for chr.trolle
4.0 years ago by
chr.trolle10
European Union
chr.trolle10 wrote:

I get the following error when trying to use autoplot {ggbio} to produce ideogram/karyogram

 autoplot(GRList, layout = "karyogram")

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘geom_alignment’ for signature ‘"data.frame"

class(GRList)

[1] "GRangesList"
attr(,"package")
[1] "GenomicRanges"

 

Genomic ranges object was recreated from GTF file:

GTFfile_GW <- makeTranscriptDbFromGFF("C:/Users/Christian Trolle/Desktop/CT/Phd in spe/RNAseq/Annotation/gc15.woPseudo.tss.gtf",
                        format="gtf",
                        exonRankAttributeName="exon_number",
                        dataSource="Gencode",
                        species="Homo sapiens",
                        circ_seqs=DEFAULT_CIRC_SEQS,
                        miRBaseBuild=NA,
                        useGenesAsTranscripts=FALSE)

GRList <- exonsBy(GTFfile_GW, by = "gene")

Seqlevels information was added like this:

 data(hg19Ideogram, package = "biovizBase")
    seqlengths(GRList) <- seqlengths(hg19Ideogram)[names(seqlengths(GRList))]

 

 autoplot(GRList, layout = "karyogram")

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘geom_alignment’ for signature ‘"data.frame"

class(GRList)

[1] "GRangesList"
attr(,"package")
[1] "GenomicRanges"

sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
 [1] XVector_0.6.0          ggbio_1.14.0           ggplot2_1.0.1         
 [4] GenomicFeatures_1.18.7 AnnotationDbi_1.28.2   Biobase_2.26.0        
 [7] GenomicRanges_1.18.4   GenomeInfoDb_1.2.5     IRanges_2.0.1         
[10] S4Vectors_0.4.0        BiocGenerics_0.12.1    edgeR_3.8.6           
[13] limma_3.22.7          

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          annotate_1.44.0         
 [3] base64enc_0.1-2          BatchJobs_1.6           
 [5] BBmisc_1.9               BiocParallel_1.0.3      
 [7] biomaRt_2.22.0           Biostrings_2.34.1       
 [9] biovizBase_1.14.1        bitops_1.0-6            
[11] brew_1.0-6               BSgenome_1.34.1         
[13] checkmate_1.5.3          cluster_2.0.1           
[15] codetools_0.2-11         colorspace_1.2-6        
[17] DBI_0.3.1                DESeq_1.18.0            
[19] dichromat_2.0-0          digest_0.6.8            
[21] fail_1.2                 foreach_1.4.2           
[23] foreign_0.8-63           Formula_1.2-1           
[25] genefilter_1.48.1        geneplotter_1.44.0      
[27] GenomicAlignments_1.2.2  GGally_0.5.0            
[29] graph_1.44.1             grid_3.1.3              
[31] gridExtra_0.9.1          gtable_0.1.2            
[33] Hmisc_3.16-0             iterators_1.0.7         
[35] lattice_0.20-31          latticeExtra_0.6-26     
[37] magrittr_1.5             MASS_7.3-40             
[39] munsell_0.4.2            nnet_7.3-9              
[41] OrganismDbi_1.8.1        plyr_1.8.2              
[43] proto_0.3-10             RBGL_1.42.0             
[45] RColorBrewer_1.1-2       Rcpp_0.11.6             
[47] RCurl_1.95-4.6           reshape_0.8.5           
[49] reshape2_1.4.1           rpart_4.1-9             
[51] Rsamtools_1.18.3         RSQLite_1.0.0           
[53] rtracklayer_1.26.3       scales_0.2.4            
[55] sendmailR_1.2-1          splines_3.1.3           
[57] stringi_0.4-1            stringr_1.0.0           
[59] survival_2.38-1          tools_3.1.3             
[61] VariantAnnotation_1.12.9 XML_3.98-1.1            
[63] xtable_1.7-4             zlibbioc_1.12.0  

 

rna-seq R • 1.3k views
ADD COMMENTlink written 4.0 years ago by chr.trolle10
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