genoPlotR: Plot Publication-Grade Gene and Genome Maps

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.

AuthorLionel Guy <lionel.guy@imbim.uu.se>
Date of publication2015-07-08 06:51:06
MaintainerLionel Guy <lionel.guy@imbim.uu.se>
LicenseGPL (>= 2)
Version0.8.4
http://genoplotr.r-forge.r-project.org/

View on R-Forge

Functions

annotation Man page
apply_color_scheme Man page
artemisColors Man page
as.annotation Man page
as.comparison Man page
as.dna_seg Man page
as.seg_plot Man page
auto_annotate Man page
barto Man page
bbone Man page
c.dna_seg Man page
chrY_subseg Man page
comparison Man page
comparisons Man page
dna_seg Man page
dna_segs Man page
gene_types Man page
genoPlotR Man page
genoPlotR-package Man page
human_nt Man page
is.annotation Man page
is.comparison Man page
is.dna_seg Man page
is.seg_plot Man page
mauve_bbone Man page
middle Man page
plot_gene_map Man page
range.annotation Man page
range.comparison Man page
range.dna_seg Man page
read_comparison_from_blast Man page
read_comparison_from_tab Man page
read_dna_seg_from_embl Man page
read_dna_seg_from_fasta Man page
read_dna_seg_from_file Man page
read_dna_seg_from_genbank Man page
read_dna_seg_from_ptt Man page
read_dna_seg_from_tab Man page
read_functions Man page
read_mauve_backbone Man page
reverse Man page
reverse.comparison Man page
reverse.default Man page
reverse.dna_seg Man page
seg_plot Man page
three_genes Man page
trim Man page
trim.annotation Man page
trim.comparison Man page
trim.default Man page
trim.dna_seg Man page
trim.seg_plot Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.