I'm encountering a persistent problem with ggbio's autoplot function using R 3.2 (I've tried both versions 3.2.2 and 3.2.3 (the latest release)). Below example provide running 64-bit R 3.2.3 on Windows 7 (full session info provided at the bottom of this post).
Specifically, I'm attempting to generate a gene model graphic by running the following code (taken from pages 5 & 6 of the Bioconductor ggbio vignette found here):
library(ggbio) library(Homo.sapiens) class(Homo.sapiens) data(genesymbol, package = "biovizBase") wh <- genesymbol[c("BRCA1", "NBR1")] wh <- range(wh, ignore.strand = TRUE) p.txdb <- autoplot(Homo.sapiens, which = wh)
I've tried fresh installs of R (3.2.2 and 3.2.3) using executables downloaded from CRAN (e.g., 3.2.2 and 3.2.3, respectively) , along with fresh installs of ggbio (and it's dependencies) through Bioconductor. Each time I attempt to run the above code, I see the following (albeit with version-specific info at top):
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(ggbio) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: ggplot2 Need specific help about ggbio? try mailing the maintainer or visit http://tengfei.github.com/ggbio/ Attaching package: ‘ggbio’ The following objects are masked from ‘package:ggplot2’: geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim Warning messages: 1: replacing previous import by ‘ggplot2::unit’ when loading ‘ggbio’ 2: replacing previous import by ‘ggplot2::arrow’ when loading ‘ggbio’ 3: replacing previous import by ‘BiocGenerics::Position’ when loading ‘ggbio’ > library(Homo.sapiens) Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GO.db Loading required package: DBI Loading required package: org.Hs.eg.db Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Now getting the GODb Object directly Now getting the OrgDb Object directly Now getting the TxDb Object directly > class(Homo.sapiens)  "OrganismDb" attr(,"package")  "OrganismDbi" > data(genesymbol, package = "biovizBase") > wh <- genesymbol[c("BRCA1", "NBR1")] > wh <- range(wh, ignore.strand = TRUE) > p.txdb <- autoplot(Homo.sapiens, which = wh) Parsing transcripts... Parsing exons... Parsing cds... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done 'select()' returned 1:1 mapping between keys and columns "gap" not in any of the valid gene feature terms "cds", "exon", "utr" Constructing graphics... Error: Unknown parameters: arrow.rate
Seems like this probably has something to do with the warning messages about ggplot2 functions rate & arrow output when loading ggbio library. I've emailed the package maintainer at the email provided here, but no reply yet. Other 'autoplot' uses for creating gene models also consistently fail with errors about unknown parameters arrow.rate and/or group.selfish. Possible this issue is related to ggbio incompatibility with the latest version of ggplot2 as mentioned here (Error when install ggbio), but suggestion of installing the ggbio binary didn't fix this for me. Any alternate suggestions greatly welcomed!
Here is my session info:
R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  org.Hs.eg.db_3.2.3 GO.db_3.2.2  RSQLite_1.0.0 DBI_0.3.1  OrganismDbi_1.12.1 GenomicFeatures_1.22.7  GenomicRanges_1.22.3 GenomeInfoDb_1.6.1  AnnotationDbi_1.32.3 IRanges_2.4.6  S4Vectors_0.8.6 Biobase_2.30.0  ggbio_1.18.1 ggplot2_2.0.0  BiocGenerics_0.16.1 loaded via a namespace (and not attached):  SummarizedExperiment_1.0.2 VariantAnnotation_1.16.4 reshape2_1.4.1  splines_3.2.3 lattice_0.20-33 colorspace_1.2-6  rtracklayer_1.30.1 RBGL_1.46.0 survival_2.38-3  XML_3.98-1.3 foreign_0.8-66 BiocParallel_1.4.3  RColorBrewer_1.1-2 lambda.r_1.1.7 plyr_1.8.3  stringr_1.0.0 zlibbioc_1.16.0 Biostrings_2.38.3  munsell_0.4.2 gtable_0.1.2 futile.logger_1.4.1  latticeExtra_0.6-26 GGally_1.0.0 biomaRt_2.26.1  BiocInstaller_1.20.1 Rcpp_0.12.2 acepack_1.3-3.3  scales_0.3.0 BSgenome_1.38.0 graph_1.48.0  Hmisc_3.17-1 XVector_0.10.0 Rsamtools_1.22.0  gridExtra_2.0.0 stringi_1.0-1 biovizBase_1.18.0  grid_3.2.3 tools_3.2.3 bitops_1.0-6  magrittr_1.5 RCurl_1.95-4.7 dichromat_2.0-0  Formula_1.2-1 cluster_2.0.3 futile.options_1.0.0  reshape_0.8.5 rpart_4.1-10 GenomicAlignments_1.6.3  nnet_7.3-11