gtrellis: Genome Level Trellis Layout
Version 1.8.0

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

AuthorZuguang Gu
Bioconductor views Sequencing Software Visualization
Date of publication2017-1-11 00:00:00
MaintainerZuguang Gu <z.gu@dkfz.de>
LicenseGPL (>= 2)
Version1.8.0
URL https://github.com/jokergoo/gtrellis
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gtrellis")

Popular man pages

add_heatmap_track: add heatmap to a new track
add_ideogram_track: Add ideogram track
add_lines_track: add lines to a new or exsited track
add_points_track: add points to a new or exsited track
add_rect_track: add retangles to a new or exsited track
add_segments_track: add segments to a new or exsited track
add_track: Add self-defined graphics track by track
See all...

All man pages Function index File listing

Man pages

add_heatmap_track: add heatmap to a new track
add_ideogram_track: Add ideogram track
add_lines_track: add lines to a new or exsited track
add_points_track: add points to a new or exsited track
add_rect_track: add retangles to a new or exsited track
add_segments_track: add segments to a new or exsited track
add_track: Add self-defined graphics track by track
current_track: The index of current track
get_cell_meta_data: Get meta data in a cell
gtrellis_layout: Initialize genome-level Trellis layout
gtrellis_show_index: Show index on each cell

Functions

add_heatmap_track Man page Source code
add_ideogram_track Man page Source code
add_lines_track Man page Source code
add_points_track Man page Source code
add_rect_track Man page Source code
add_segments_track Man page Source code
add_track Man page Source code
almost_equal Source code
current_track Man page Source code
get_cell_meta_data Man page Source code
get_plot_index Source code
gtrellis_layout Man page Source code
gtrellis_show_index Man page Source code
increase_plot_index Source code
is_intersected Source code
is_on_bottom Source code
is_on_left Source code
is_on_right Source code
is_on_top Source code
normalizeToGRanges Source code
partition Source code
re_calculate_xlim Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/custimized_track.R
R/global.R
R/layout.R
R/partition.R
R/track.R
TODO
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/gtrellis.R
inst/doc/gtrellis.Rmd
inst/doc/gtrellis.html
inst/extdata
inst/extdata/df_control.rds
inst/extdata/df_tumor.rds
inst/extdata/gencode_v19_protein_coding_genes.rds
inst/extdata/gwasCatalog.RData
inst/tests
man
man/add_heatmap_track.rd
man/add_ideogram_track.rd
man/add_lines_track.rd
man/add_points_track.rd
man/add_rect_track.rd
man/add_segments_track.rd
man/add_track.rd
man/current_track.rd
man/get_cell_meta_data.rd
man/gtrellis_layout.rd
man/gtrellis_show_index.rd
test
tests
tests/test-all.R
tests/testthat
tests/testthat/test_layout.R
vignettes
vignettes/custom.css
vignettes/gtrellis.Rmd
gtrellis documentation built on May 20, 2017, 11 p.m.

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