genoPlotR changes ================= 0.8.11 - 2021-01-05 ------------------- Small fix: - Replaced calls to order() on data.frames by do.call(order, list=...) to comply with the latest R developments. 0.8.10 - 2020-12-10 ------------------- Small fix: - Removed calls to cairo_pdf(), replaced with standard pdf() 0.8.9 - 2019-01-16 ------------------ Fixing colors in the examples: col is now mapping to "col" and not to "fill", and affects the example data (which has "col"). 0.8.8 - 2018-02-21 ------------------ Small fix: - pkg/man/genoPlotR-package.Rd had to be modified not to be unsynched with DESCRIPTION 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