NEWS

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genoPlotR 0.8.11 (2021-01-07)

Small fix

• Replaced calls to order() on data.frames by do.call(order, list=...) to comply with the latest R developments.

genoPlotR 0.8.10 (2020-12-10)

Small fix

• Removed calls to cairo_pdf(), replaced with standard pdf()

genoPlotR 0.8.9 (2019-01-25)

Fixing colors in the examples: col is now mapping to "col" and not to "fill

and affects the example data (which has "col

genoPlotR 0.8.8

Small fix

• pkg/man/genoPlotR-package.Rd had to be modified not to be unsynched with DESCRIPTION

genoPlotR 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

genoPlotR 0.8.6 (2017-05-16)

Previous version created warnings with R 3.4.0. Removed the inst/doc

folder on R-forge. Package back on CRAN

genoPlotR 0.8.3

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

genoPlotR 0.8.2 (2013-12-23)

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

genoPlotR 0.8.1

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.

genoPlotR 0.8 (2012-06-25)

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

genoPlotR 0.7.1

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

genoPlotR 0.7 (2011-05-03)

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

genoPlotR 0.6.1 (2011-03-31)

BUGFIX

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

genoPlotR 0.6 (2011-03-24)

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

genoPlotR 0.5.8

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

genoPlotR 0.5.7

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)

genoPlotR 0.5.6

BUGFIX

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

genoPlotR 0.5.5

NEW FEATURES

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

genoPlotR 0.5.4 (2010-09-22)

BUGFIX

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

genoPlotR 0.5.3

Article published in Bioinformatics, added a CITATION file

genoPlotR 0.5.2

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

genoPlotR 0.5.1 (2010-08-16)

BUGFIX

• Added aliases in the documentation to avoid warnings when compiling

genoPlotR 0.5 (2010-06-24)

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

genoPlotR 0.4.1

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.

genoPlotR 0.4 (2010-05-19)

NEW FEATURES

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

genoPlotR 0.3

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

genoPlotR 0.2

Initial commit to R-Forge