Learn R Programming

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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

1.16.1

License

Artistic-2.0

Maintainer

Tengfei Yin

Last Published

February 15th, 2017

Functions in ggbio (1.16.1)

geom_bar

Segment geoms for GRanges object
geom_rect

Rect geoms for GRanges object
geom_segment

Segment geoms for GRanges object
layout_circle

Create a circle layout
layout_karyogram

Create a karyogram layout
geom_chevron

Chevron geoms for GRanges object
GGbio

class ggbio
stat_aggregate

Generates summaries on the specified windows
ggplot

ggplot generic method
stat_bin

Binning method
stat_coverage

Calculate coverage
stat_gene

Calculate gene structure
rescale

rescale ggplot object
scale_fill_fold_change

scale color for fold change values
stat_identity

Transform the data to a data.frame and for multiple geoms.
stat_mismatch

Calculate mismatch summary
geom_alignment

Alignment geoms for GRanges object
geom_arch

Arch geoms for GRanges object
theme

theme in ggbio
Tracked

Tracked class
tracks

Tracks for genomic graphics
geom_arrow

Arrow geoms for GRanges object
geom_arrowrect

Arrowrect geoms for GRanges object
ggsave

Save a ggplot object or tracks with sensible defaults
Grob-class

Grob getter
Ideogram

Plot single chromosome with cytoband
plotRangesLinkedToData

Plot Ranges Linked with Data
arrangeGrobByParsingLegend

Arrange grobs by parse their legend.
autoplot

Generic autoplot function
plotFragLength

Plot estimated fragment length for paired-end RNA-seq data
plotGrandLinear

Manhattan for GWAS
scale_fill_giemsa

scale filled color to customized giemsa color.
scale_x_sequnit

scale x by unit
stat_reduce

Reduce an object.
stat_slice

Slice Rle/RleList to view them as bar or heatmap.
zoom

Simple navigation for ggbio object.
Plot

Plot class
plotStackedOverview

Plot stacked overview
plotSpliceSum

Plot Splice Summary from RNA-seq data
stat_stepping

Calculate stepping levels
stat_table

Tabulate a GRanges object