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
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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

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