genoPlotR: Plot Publication-Grade Gene and Genome Maps
Version 0.8.6

Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.

Browse man pages Browse package API and functions Browse package files

AuthorLionel Guy <lionel.guy@imbim.uu.se>
Date of publication2017-05-16 08:56:55 UTC
MaintainerLionel Guy <lionel.guy@imbim.uu.se>
LicenseGPL (>= 2)
Version0.8.6
URL http://genoplotr.r-forge.r-project.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("genoPlotR")

Man pages

annotation: Annotation class and class functions
apply_color_scheme: Apply a color scheme
artemisColors: Artemis Colors
auto_annotate: Auto-annotate dna_segs
barto: Comparison of 4 Bartonella genomes
c.dna_seg: Concatenate dna_seg objects
chrY_subseg: Comparisons of subsegments of the Y chromosome in human and...
comparison: Comparison class and class functions
dna_seg: DNA segment (dna_seg) class and class functions
gene_types: Gene types
genoPlotR-package: genoPlotR - a R framework to produce publication-grade maps...
human_nt: Human-readable nucleotide scale
mauve_bbone: Mauve backbone of 4 Bartonella genomes
middle: Middles of a dna_seg
plot_gene_map: Plot gene and genome maps
range: Range calculation
read_functions: Reading functions
reverse: Reverse objects
seg_plot: seg_plot class and class functions
three_genes: Three genes data set
trim: Trimming data frames or more complex objects with >= 2...

Functions

annotation Man page Source code
annotation_grob Source code
apply_color_scheme Man page Source code
arrow_coord Source code
artemisColors Man page Source code
as.annotation Man page Source code
as.comparison Man page Source code
as.dna_seg Man page Source code
as.seg_plot Man page Source code
auto_annotate Man page Source code
auto_gene_type Source code
barto Man page
bbone Man page
block_coord Source code
bracket_coord Source code
c.dna_seg Man page Source code
calc_comp_coor Source code
chrY_subseg Man page
comparison Man page Source code
comparison_grob Source code
comparisons Man page
dna_seg Man page Source code
dna_seg_grob Source code
dna_seg_label_grob Source code
dna_seg_scale_grob Source code
dna_segs Man page
exon_coord Source code
extract_data Source code
gap_grob Source code
gene_grob Source code
gene_types Man page Source code
genoPlotR Man page
genoPlotR-package Man page
get_end Source code
get_start Source code
human_nt Man page Source code
is.annotation Man page Source code
is.comparison Man page Source code
is.dna_seg Man page Source code
is.seg_plot Man page Source code
label_grob Source code
mauve_bbone Man page
middle Man page Source code
minimize_comps Source code
nice_ylim.seg_plot Source code
permute_tree Source code
phylog_grob Source code
plot_gene_map Man page Source code
range.annotation Man page Source code
range.comparison Man page Source code
range.dna_seg Man page Source code
read_comparison Source code
read_comparison_from_blast Man page Source code
read_comparison_from_tab Man page Source code
read_dna_seg Source code
read_dna_seg_from_embl Man page Source code
read_dna_seg_from_fasta Man page Source code
read_dna_seg_from_file Man page Source code
read_dna_seg_from_genbank Man page Source code
read_dna_seg_from_ptt Man page Source code
read_dna_seg_from_tab Man page Source code
read_functions Man page
read_mauve_backbone Man page Source code
reverse Man page Source code
reverse.comparison Man page Source code
reverse.default Man page Source code
reverse.dna_seg Man page Source code
scale_grob Source code
seg_plot Man page Source code
similarity_grob Source code
three_genes Man page
trim Man page Source code
trim.annotation Man page Source code
trim.comparison Man page Source code
trim.default Man page Source code
trim.dna_seg Man page Source code
trim.seg_plot Man page Source code
yaxis_coords Source code
yaxis_grob Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/barto.backbone
inst/extdata/BH_vs_BQ.blastn.tab
inst/extdata/barto.guide_tree
inst/extdata/barto.sh
inst/extdata/comparison2.tab
inst/extdata/dna_seg3.tab
inst/extdata/BG_plasmid.embl
inst/extdata/BG_plasmid.gbk
inst/extdata/BQ.ptt
inst/extdata/mauve.sh
inst/doc
inst/doc/genoPlotR.R
inst/doc/genoPlotR.Rnw
inst/doc/genoPlotR.pdf
NAMESPACE
NEWS
data
data/barto.RData
data/three_genes.RData
data/chrY_subseg.RData
data/mauve_bbone.RData
R
R/read_mauve_backbone.R
R/annotation.R
R/color_schemes.R
R/plot_helpers.R
R/comparison.R
R/generic.R
R/read_dna_seg.R
R/grobs.R
R/seg_plot.R
R/genoPlotR.R
R/read_comparison.R
R/minimize_comps.R
R/dna_seg.R
R/auto_annotate.R
R/similarity.R
R/gene_types.R
R/gene.R
R/phylog_grob.R
vignettes
vignettes/Bioinformatics-2010-Guy-2334-5.pdf
vignettes/genoPlotR.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/annotation.Rd
man/dna_seg.Rd
man/seg_plot.Rd
man/reverse.Rd
man/gene_types.Rd
man/chrY_subseg.Rd
man/middle.Rd
man/three_genes.Rd
man/barto.Rd
man/human_nt.Rd
man/comparison.Rd
man/apply_color_scheme.Rd
man/mauve_bbone.Rd
man/c.dna_seg.Rd
man/trim.Rd
man/auto_annotate.Rd
man/range.Rd
man/read_functions.Rd
man/genoPlotR-package.Rd
man/plot_gene_map.Rd
man/artemisColors.Rd
genoPlotR documentation built on May 29, 2017, 4:20 p.m.