Entering edit mode
8.8 years ago
chr.trolle
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10
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