Version: 0.8.11 Date: 2021-01-07 Category: Small fix Text: Replaced calls to order() on data.frames by do.call(order, list=...) to comply with the latest R developments. Version: 0.8.10 Date: 2020-12-10 Category: Small fix Text: Removed calls to cairo_pdf(), replaced with standard pdf() Version: 0.8.9 Date: 2019-01-25 Category: Fixing colors in the examples: col is now mapping to "col" and not to "fill Text: Version: 0.8.9 Date: 2019-01-25 Category: and affects the example data (which has "col Text: Version: 0.8.8 Category: Small fix Text: pkg/man/genoPlotR-package.Rd had to be modified not to be unsynched with DESCRIPTION Version: 0.8.7 Date: 2017-11-06 Category: Small bug fixes Text: Changed CITATION to comply with as.person() requirements Version: 0.8.7 Date: 2017-11-06 Category: Small bug fixes Text: Corrected a line too long in dna_segs.Rd Version: 0.8.7 Date: 2017-11-06 Category: Small bug fixes Text: Corrected broken links in the vignette Version: 0.8.6 Date: 2017-05-16 Category: Previous version created warnings with R 3.4.0. Removed the inst/doc Text: Version: 0.8.6 Date: 2017-05-16 Category: folder on R-forge. Package back on CRAN Text: Version: 0.8.3 Category: Adapting the package to new CRAN guidelines Text: Imports instead of Depends (imported packages) Version: 0.8.3 Category: Adapting the package to new CRAN guidelines Text: Cleaned up DESCRIPTION, updated email address Version: 0.8.3 Category: Adapting the package to new CRAN guidelines Text: Restored some functions on the webpage Version: 0.8.2 Date: 2013-12-23 Category: Adapting the package to new CRAN guidelines Text: Moved vignette from inst/doc/ to vignettes/ Version: 0.8.2 Date: 2013-12-23 Category: Adapting the package to new CRAN guidelines Text: Reduced examples in plot_gene_map to get under 5s checking time Version: 0.8.1 Category: BUGFIXES Text: Fixed a bug in read_mauve_backbone where the reference genome could be set to anything. Added check for that. Version: 0.8.1 Category: BUGFIXES Text: Fixed a bug in apply_color_schemes and the main function, to prevent comparisons with 0 rows to crash the program. Version: 0.8 Date: 2012-06-25 Category: NEW FEATURE Text: Comparisons that overlap xlims are now included and trimmed inside xlims Version: 0.8 Date: 2012-06-25 Category: BUGFIXES Text: Automatic horizontal placement of dna_segs had some error in certain conditions Version: 0.8 Date: 2012-06-25 Category: BUGFIXES Text: Reading artemis colors could not be overriden Version: 0.8 Date: 2012-06-25 Category: BUGFIXES Text: Error handling when reading null tables Version: 0.7.1 Category: NEW FEATURE Text: A scale can be added to the tree (argument tree_scale) Version: 0.7.1 Category: BUGFIX Text: Arguments ylim (of seg_plot objects) were not taken into account when plotting Version: 0.7 Date: 2011-05-03 Category: NEW FEATURES Text: 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 Version: 0.7 Date: 2011-05-03 Category: NEW FEATURES Text: Added a function, auto_annotate, to create smart annotations from genbank or embl files. Version: 0.7 Date: 2011-05-03 Category: NEW FEATURES Text: Added the possibility to use user-defined graphical functions to plot genes. Version: 0.7 Date: 2011-05-03 Category: NEW FEATURES Text: Extra fields (tags) can be parsed from genbank and embl files. Version: 0.7 Date: 2011-05-03 Category: BUGFIX Text: The last line of the features was not read in genbank and embl files Version: 0.6.1 Date: 2011-03-31 Category: BUGFIX Text: Vignette contained non-ASCII characters Version: 0.6.1 Date: 2011-03-31 Category: BUGFIX Text: Fixed an incoherent variable name in arrow_coord Version: 0.6 Date: 2011-03-24 Category: NEW FEATURES Text: Added transparency support in apply_color_scheme, which is applied by default. Version: 0.6 Date: 2011-03-24 Category: NEW FEATURES Text: Added a function, artemisColors(), that returns the colors as in Artemis. Version: 0.6 Date: 2011-03-24 Category: NEW FEATURES Text: read_dna_seg_from_file can now read color or colour tags in genbank or embl files. Version: 0.6 Date: 2011-03-24 Category: NEW FEATURES Text: Added experimental support for tree branches annotations. Version: 0.6 Date: 2011-03-24 Category: BUGFIX Text: Further corrected a bug occuring when fixed_gap_length was set, and allowing comparisons with 0 rows. Version: 0.6 Date: 2011-03-24 Category: BUGFIX Text: Fasta types were incorrectly guessed Version: 0.6 Date: 2011-03-24 Category: NOTE: some of the features have been released in an intermediate version 0.5.9 Text: Version: 0.5.8 Category: NEW FEATURE Text: The plot area is now clipped, as a workaround to avoid comparisons that are too large. Version: 0.5.8 Category: BUGFIX Text: Corrected a bug occuring when fixed_gap_length was set Version: 0.5.7 Category: BUGFIX Text: Corrected as.dna_seg to prevent factors to slip in and fixed the gene_type verification. Version: 0.5.7 Category: NEW FEATURE Text: Changing the color of the dna_labels is possible (not for trees yet) Version: 0.5.6 Category: BUGFIX Text: Modified the feature parsing algorithm, features with an "_" inside (ex. misc_feature) were parsed incorrectly. Version: 0.5.5 Category: NEW FEATURES Text: Added a new gene_type: lines (and the corresponding side_lines) Version: 0.5.5 Category: NEW FEATURES Text: Improved the example for gene_type Version: 0.5.4 Date: 2010-09-22 Category: BUGFIX Text: Added some extra checks on mauve input data, and on dna_seg input data to avoid mysterious error messages Version: 0.5.3 Category: Article published in Bioinformatics, added a CITATION file Text: Version: 0.5.2 Category: NEW FEATURES Text: Added read_dna_seg_from_fasta, that can read a fasta file and return one segment of the corresponding length Version: 0.5.2 Category: NEW FEATURES Text: 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. Version: 0.5.2 Category: BUGFIX Text: Corrected a bug that provoked errors in displaying subsegments that were closer to each other than the gap length Version: 0.5.1 Date: 2010-08-16 Category: BUGFIX Text: Added aliases in the documentation to avoid warnings when compiling Version: 0.5 Date: 2010-06-24 Category: NEW FEATURES Text: New argument to plot_gene_map: n_scale_ticks, gives the approx. number of ticks in the dna_seg_scales Version: 0.5 Date: 2010-06-24 Category: NEW FEATURES Text: New argument to plot_gene_map: scale_cex, allows to change the size of the labels in dna_seg_scales Version: 0.5 Date: 2010-06-24 Category: NEW FEATURES Text: 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 Version: 0.4.1 Category: BUGFIX Text: 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. Version: 0.4 Date: 2010-05-19 Category: NEW FEATURES Text: Add the multisegment support Version: 0.4 Date: 2010-05-19 Category: NEW FEATURES Text: dna_scales, annotations on all the segments, Version: 0.4 Date: 2010-05-19 Category: NEW FEATURES Text: Generated new examples. Version: 0.3 Category: NEW FEATURES Text: On plot_gene_maps, it is now possible to add automatic scale to any or all dna_segments. Version: 0.3 Category: NEW FEATURES Text: It is possible (and recommended) to apply "global" color scheme at the time of plotting (and not when parsing comparisons). Version: 0.3 Category: INTERNALS Text: Application of color schemes is now more rational Version: 0.3 Category: INTERNALS Text: Named every element and viewport, so its easier to navigate Version: 0.3 Category: INTERNALS Text: Removed dependancies to RColorBrewer Version: 0.2 Category: Initial commit to R-Forge Text: