ggbio v1.20.0
Visualization tools for genomic data.
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.
Readme
INSTALL
For R 2.15 with git version ggbio(latest)
This is for developers, notice I am not using bioc-devel svn as major version control system. If you want to play with latest ggbio you have to stick with this method.
Install of developmental version of ggbio require developmental R now. Simply open R session and run the following code:
source("http://www.tengfei.name/projects/ggbio/utils/installer.R")
This will install ggplot2/ggbio github version, and bioc-dev version denpendencies.
For all users, make sure to install R package RCurl to use this command
For Windows users: if you came across buiding errors, please install Rtools, then run the command line again.
For R 2.15 with bioc-dev version ggbio
source("http://bioconductor.org/biocLite.R")
biocLite("ggbio")
This will automatically install the right bioc-dev version of ggbio
This is currently now working due to the new-yet-unreleased ggplot2 0.9
For R 2.14
source("http://bioconductor.org/biocLite.R")
biocLite("ggbio")
not supported yet for git hub version ggbio
Functions in ggbio
| Name | Description | |
| geom_alignment | Alignment geoms for GRanges object | |
| geom_arch | Arch geoms for GRanges object | |
| scale_fill_giemsa | scale filled color to customized giemsa color. | |
| scale_x_sequnit | scale x by unit | |
| Tracked | Tracked class | |
| theme | theme in ggbio | |
| plotFragLength | Plot estimated fragment length for paired-end RNA-seq data | |
| plotGrandLinear | Manhattan for GWAS | |
| scale_fill_fold_change | scale color for fold change values | |
| rescale | rescale ggplot object | |
| stat_table | Tabulate a GRanges object | |
| stat_stepping | Calculate stepping levels | |
| tracks | Tracks for genomic graphics | |
| geom_chevron | Chevron geoms for GRanges object | |
| geom_bar | Segment geoms for GRanges object | |
| layout_circle | Create a circle layout | |
| layout_karyogram | Create a karyogram layout | |
| geom_arrow | Arrow geoms for GRanges object | |
| geom_arrowrect | Arrowrect geoms for GRanges object | |
| zoom | Simple navigation for ggbio object. | |
| Plot | Plot class | |
| stat_reduce | Reduce an object. | |
| stat_slice | Slice Rle/RleList to view them as bar or heatmap. | |
| plotSpliceSum | Plot Splice Summary from RNA-seq data | |
| plotStackedOverview | Plot stacked overview | |
| geom_rect | Rect geoms for GRanges object | |
| GGbio | class ggbio | |
| ggplot | ggplot methods | |
| geom_segment | Segment geoms for GRanges object | |
| Ideogram | Plot single chromosome with cytoband | |
| plotRangesLinkedToData | Plot Ranges Linked with Data | |
| stat_identity | Transform the data to a data.frame and for multiple geoms. | |
| stat_mismatch | Calculate mismatch summary | |
| arrangeGrobByParsingLegend | Arrange grobs by parse their legend. | |
| autoplot | Generic autoplot function | |
| ggsave | Save a ggplot object or tracks with sensible defaults | |
| Grob-class | Grob getter | |
| stat_aggregate | Generates summaries on the specified windows | |
| stat_bin | Binning method | |
| stat_coverage | Calculate coverage | |
| stat_gene | Calculate gene structure | |
| No Results! | ||
Last year downloads
Details
| VignetteBuilder | knitr |
| 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 |
| imports | AnnotationDbi , Biobase , Biostrings , biovizBase (>= 1.19.1) , BSgenome , ensembldb (>= 1.3.8) , GenomeInfoDb (>= 1.1.3) , GenomicAlignments (>= 1.1.16) , GenomicFeatures (>= 1.17.13) , GenomicRanges (>= 1.21.10) , GGally , graphics , grDevices , grid , gridExtra , gtable , Hmisc , IRanges , OrganismDbi , reshape2 , Rsamtools (>= 1.17.28) , rtracklayer (>= 1.25.16) , S4Vectors (>= 0.9.25) , scales , stats , SummarizedExperiment , utils , VariantAnnotation (>= 1.11.4) |
| depends | BiocGenerics , ggplot2 (>= 1.0.0) , methods |
| suggests | BiocStyle , BSgenome.Hsapiens.UCSC.hg19 , chipseq , EnsDb.Hsapiens.v75 , Homo.sapiens , knitr , testthat , TxDb.Hsapiens.UCSC.hg19.knownGene , TxDb.Mmusculus.UCSC.mm9.knownGene , vsn |
| Contributors | Michael Lawrence, Dianne Cook, Tengfei Yin, Johannes Rainer |
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