genoPlotR: Plot Publication-Grade Gene and Genome Maps

Share:

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.

Author
Lionel Guy <lionel.guy@imbim.uu.se>
Date of publication
2015-07-08 06:51:06
Maintainer
Lionel Guy <lionel.guy@imbim.uu.se>
License
GPL (>= 2)
Version
0.8.4
URLs

View on R-Forge

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...

Files in this package

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