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

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

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

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.

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

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

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

BUGFIX:

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

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

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

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)

BUGFIX:

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

NEW FEATURES:

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

BUGFIX:

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

Article published in Bioinformatics, added a CITATION file.

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

BUGFIX:

  • Added aliases in the documentation to avoid warnings when compiling

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

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.

NEW FEATURES:

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

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

Initial commit to R-Forge

Reference manual

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install.packages("genoPlotR")

0.8.6 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.guy@imbim.uu.se>


Documentation:   PDF Manual  


GPL (>= 2) license


Imports methods

Depends on ade4, grid


See at CRAN