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.


News

genoPlotR changes

0.8.7 - 2017-11-06

Small bug fixes:

  • Changed CITATION to comply with as.person() requirements
  • Corrected a line too long in dna_segs.Rd
  • Corrected broken links in the vignette

0.8.6 - 2017-05-15

Previous version created warnings with R 3.4.0. Removed the inst/doc folder on R-forge. Package back on CRAN.

0.8.3 - 2015-07-02

Adapting the package to new CRAN guidelines:

  • Imports instead of Depends (imported packages)
  • Cleaned up DESCRIPTION, updated email address
  • Restored some functions on the webpage

0.8.2 - 2013-12-19

Adapting the package to new CRAN guidelines:

  • Moved vignette from inst/doc/ to vignettes/
  • Reduced examples in plot_gene_map to get under 5s checking time

0.8.1 - 2012-11-19

BUGFIXES:

  • Fixed a bug in read_mauve_backbone where the reference genome could be set to anything. Added check for that.
  • Fixed a bug in apply_color_schemes and the main function, to prevent comparisons with 0 rows to crash the program.

0.8 - 2012-06-21

NEW FEATURE:

  • Comparisons that overlap xlims are now included and trimmed inside xlims BUGFIXES:
  • Automatic horizontal placement of dna_segs had some error in certain conditions
  • Reading artemis colors could not be overriden
  • Error handling when reading null tables

0.7.1 - 2011-05-04

NEW FEATURE:

  • A scale can be added to the tree (argument tree_scale) BUGFIX:
  • Arguments ylim (of seg_plot objects) were not taken into account when plotting

0.7 - 2011-04-18

NEW FEATURES:

  • It is now possible to plot user-defined graphs on top of each dna_seg, using the graphical functions of grid or user-defined ones. See seg_plot functions and argument in plot_gene_maps
  • Added a function, auto_annotate, to create smart annotations from genbank or embl files.
  • Added the possibility to use user-defined graphical functions to plot genes.
  • Extra fields (tags) can be parsed from genbank and embl files. BUGFIX:
  • The last line of the features was not read in genbank and embl files

0.6.1 - 2011-03-30

BUGFIX:

  • Vignette contained non-ASCII characters
  • Fixed an incoherent variable name in arrow_coord

0.6 - 2011-03-16

NEW FEATURES:

  • Added transparency support in apply_color_scheme, which is applied by default.
  • Added a function, artemisColors(), that returns the colors as in Artemis.
  • read_dna_seg_from_file can now read color or colour tags in genbank or embl files.
  • Added experimental support for tree branches annotations. BUGFIX:
  • Further corrected a bug occuring when fixed_gap_length was set, and allowing comparisons with 0 rows.
  • Fasta types were incorrectly guessed NOTE: some of the features have been released in an intermediate version 0.5.9

0.5.8 - 2011-01-31

NEW FEATURE:

  • The plot area is now clipped, as a workaround to avoid comparisons that are too large. BUGFIX:
  • Corrected a bug occuring when fixed_gap_length was set

0.5.7 - 2010-12-16

BUGFIX:

  • Corrected as.dna_seg to prevent factors to slip in and fixed the gene_type verification. NEW FEATURE:
  • Changing the color of the dna_labels is possible (not for trees yet)

0.5.6 - 2010-10-04

BUGFIX:

  • Modified the feature parsing algorithm, features with an "_" inside (ex. misc_feature) were parsed incorrectly.

0.5.5 - 2010-09-27

NEW FEATURES:

  • Added a new gene_type: lines (and the corresponding side_lines)
  • Improved the example for gene_type

0.5.4 - 2010-09-15

BUGFIX:

  • Added some extra checks on mauve input data, and on dna_seg input data to avoid mysterious error messages

0.5.3 - 2010-09-08

Article published in Bioinformatics, added a CITATION file.

0.5.2 - 2010-08-24

NEW FEATURES:

  • Added read_dna_seg_from_fasta, that can read a fasta file and return one segment of the corresponding length
  • Added two arguments to plot_gene_map, to allow to define the minimum gap length and to allow to have fixed gap length but still automating the placement of the whole segment. BUGFIX:
  • Corrected a bug that provoked errors in displaying subsegments that were closer to each other than the gap length

0.5.1 - 2010-08-19

BUGFIX:

  • Added aliases in the documentation to avoid warnings when compiling

0.5 - 2010-06-14

NEW FEATURES:

  • New argument to plot_gene_map: n_scale_ticks, gives the approx. number of ticks in the dna_seg_scales
  • New argument to plot_gene_map: scale_cex, allows to change the size of the labels in dna_seg_scales
  • New argument to plot_gene_map: dna_seg_label_cex, allows to change the size of the labels in the tree or dna_seg_labels

0.4.1 - 2010-06-01

BUGFIX:

  • Added support for large phylogenetic trees. Given the mandatory use of enum.phylog to permute the trees to fit the labels with the dna_seg labels, big trees (requiring more than 1000 permutations) broke the program. Now either the tree is permutable, in the right order, or an error is thrown.

0.4 - 2010-04-19

NEW FEATURES:

  • Add the multisegment support
  • dna_scales, annotations on all the segments,
  • Generated new examples.

0.3 - 2010-04-09

NEW FEATURES:

  • On plot_gene_maps, it is now possible to add automatic scale to any or all dna_segments.
  • It is possible (and recommended) to apply "global" color scheme at the time of plotting (and not when parsing comparisons). INTERNALS:
  • Application of color schemes is now more rational
  • Named every element and viewport, so its easier to navigate
  • Removed dependancies to RColorBrewer

0.2 - 2010-01-11

Initial commit to R-Forge

Reference manual

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install.packages("genoPlotR")

0.8.7 by Lionel Guy, 4 months ago


http://genoplotr.r-forge.r-project.org/


Browse source code at https://github.com/cran/genoPlotR


Authors: Lionel Guy <lionel.g[email protected]>


Documentation:   PDF Manual  


GPL (>= 2) license


Imports methods

Depends on ade4, grid


See at CRAN