Learn R Programming

⚠️There's a newer version (1.20.1) of this package.Take me there.

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

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Version

Version

1.20.0

License

Artistic-2.0

Maintainer

Michael Lawrence

Last Published

February 15th, 2017

Functions in ggbio (1.20.0)

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