ggbio

Package: ggbio
Version: 1.20.1
Title: Visualization tools for genomic data.
Description: The ggbio package extends and specializes the grammar of
graphics for biological data. The graphics are designed to
answer common scientific questions, in particular those often
asked of high throughput genomics data. All core Bioconductor
data structures are supported, where appropriate. The package
supports detailed views of particular genomic regions, as well
as genome-wide overviews. Supported overviews include ideograms
and grand linear views. High-level plots include sequence
fragment length, edge-linked interval to data view, mismatch
pileup, and several splicing summaries.
Authors@R: c(person("Tengfei", "Yin", role=c("aut"),
email="yintengfei@gmail.com"),
person("Michael", "Lawrence", role=c("aut", "ths", "cre"),
email="lawrence.michael@gene.com"),
person("Dianne", "Cook", role=c("aut", "ths")),
person("Johannes", "Rainer", role="ctb"))
Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0)
Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales,
reshape2, gtable, Hmisc, biovizBase (>= 1.19.1), Biobase,
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb (>= 1.1.3),
GenomicRanges (>= 1.21.10), SummarizedExperiment, Biostrings,
Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16),
BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>=
1.25.16), GenomicFeatures (>= 1.17.13), OrganismDbi, GGally,
ensembldb (>= 1.3.8), AnnotationDbi
VignetteBuilder: knitr
Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq,
TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat,
EnsDb.Hsapiens.v75
URL: http://tengfei.github.com/ggbio/
BugReports: https://github.com/tengfei/ggbio/issues
License: Artistic-2.0
LazyLoad: Yes
Collate: AllClasses.R AllGenerics.R Cache-class.R GGbio-class.R
Grob-class.R ideogram.R Tracked-class.R Plot-class.R
ggplot-method.R theme.R Tracks-class.R geom_chevron-method.R
geom_alignment-method.R geom_arch-method.R geom_arrow-method.R
geom_arrowrect-method.R geom_rect-method.R
geom_segment-method.R geom_bar-method.R layout_circle-method.R
layout_karyogram-method.R layout_linear-method.R
stat_aggregate-method.R stat_coverage-method.R
stat_identity-method.R stat_mismatch-method.R
stat_stepping-method.R stat_gene-method.R stat_table-method.R
stat_bin-method.R stat_slice-method.R stat_reduce-method.R
coord_genome-method.R autoplot-method.R hack.R
plotGrandLinear.R plotRangesLinkedToData.R
plotFragLength-method.R plotSpliceSum-method.R rescale-method.R
utils.R zzz.R
biocViews: Infrastructure, Visualization
NeedsCompilation: no
Packaged: 2016-05-16 03:06:32 UTC; biocbuild
Author: Tengfei Yin [aut],
Michael Lawrence [aut, ths, cre],
Dianne Cook [aut, ths],
Johannes Rainer [ctb]
Maintainer: Michael Lawrence <lawrence.michael@gene.com>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ggbio' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: subclass "ExonrankFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "ExonrankFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a generic function for 'print' from package 'base' in package 'ggbio'
Creating a new generic function for 'geom_rect' in package 'ggbio'
Creating a new generic function for 'geom_segment' in package 'ggbio'
Creating a new generic function for 'geom_bar' in package 'ggbio'
Creating a new generic function for 'stat_identity' in package 'ggbio'
Creating a new generic function for 'stat_bin' in package 'ggbio'
** help
*** installing help indices
  converting help for package 'ggbio'
    finding HTML links ... done
    Grob-class                              html  
    Plot-class                              html  
    Tracked-class                           html  
    arrangeGrobByParsingLegend              html  
    autoplot-method                         html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/autoplot-method.Rd:310: missing file link 'EnsDb'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/autoplot-method.Rd:378: missing file link 'EnsDb'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/autoplot-method.Rd:413: missing file link 'EnsDb'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/autoplot-method.Rd:417: missing file link 'EnsDb'
    geom_alignment-method                   html  
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/geom_alignment-method.Rd:61: missing file link 'BasicFilter-class'
    geom_arch-method                        html  
    geom_arrow-method                       html  
    geom_arrowrect-method                   html  
    geom_bar-method                         html  
    geom_chevron-method                     html  
    geom_rect-method                        html  
    geom_segment-method                     html  
    ggbio-class                             html  
    ggplot-method                           html  
    ggsave                                  html  
    layout_circle-method                    html  
    layout_karyogram-method                 html  
    nav                                     html  
    plotFragLength                          html  
    plotGrandLinear                         html  
    plotRangesLinkedToData                  html  
    plotSingleChrom                         html  
    plotSpliceSum                           html  
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/plotSpliceSum.Rd:26: missing file link 'EnsDb'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/plotSpliceSum.Rd:30: missing file link 'BasicFilter-class'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/plotSpliceSum.Rd:36: missing file link 'EnsDb'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/plotSpliceSum.Rd:38: missing file link 'BasicFilter-class'
    plotStackedOverview                     html  
    rescale-method                          html  
    scale_fill_fold_change                  html  
    scale_fill_giemsa                       html  
    scale_x_sequnit                         html  
    stat_aggregate-method                   html  
    stat_bin-method                         html  
    stat_coverage-method                    html  
    stat_gene-method                        html  
    stat_identity-method                    html  
    stat_mismatch-method                    html  
    stat_reduce-method                      html  
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_reduce-method.Rd:45: missing file link 'reduce'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_reduce-method.Rd:48: missing file link 'reduce'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_reduce-method.Rd:51: missing file link 'reduce'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_reduce-method.Rd:54: missing file link 'reduce'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_reduce-method.Rd:64: missing file link 'reduce'
    stat_slice-method                       html  
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_slice-method.Rd:66: missing file link 'slice'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_slice-method.Rd:69: missing file link 'slice'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_slice-method.Rd:72: missing file link 'slice'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_slice-method.Rd:75: missing file link 'slice'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_slice-method.Rd:78: missing file link 'slice'
Rd warning: /tmp/RtmpStgikk/R.INSTALL6662349d83d/ggbio/man/stat_slice-method.Rd:85: missing file link 'slice'
    stat_stepping-method                    html  
    stat_table-method                       html  
    theme                                   html  
    tracks                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (ggbio)
Making 'packages.html' ... done