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.
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
- 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.
- Comparisons that overlap xlims are now included and trimmed inside
- Automatic horizontal placement of dna_segs had some error in certain
- Reading artemis colors could not be overriden
- Error handling when reading null tables
- A scale can be added to the tree (argument tree_scale)
- Arguments ylim (of seg_plot objects) were not taken into account
- 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
- Extra fields (tags) can be parsed from genbank and embl files.
- The last line of the features was not read in genbank and embl files
- Vignette contained non-ASCII characters
- Fixed an incoherent variable name in arrow_coord
- Added transparency support in apply_color_scheme, which is applied by
- 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
- Added experimental support for tree branches annotations.
- 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
- The plot area is now clipped, as a workaround to avoid comparisons that
are too large.
- Corrected a bug occuring when fixed_gap_length was set
- Corrected as.dna_seg to prevent factors to slip in and fixed the gene_type
- Changing the color of the dna_labels is possible (not for trees yet)
- Modified the feature parsing algorithm, features with an "_" inside (ex.
misc_feature) were parsed incorrectly.
- Added a new gene_type: lines (and the corresponding side_lines)
- Improved the example for gene_type
- 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.
- 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.
- Corrected a bug that provoked errors in displaying subsegments that were
closer to each other than the gap length
- Added aliases in the documentation to avoid warnings when compiling
- 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
- 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
- Add the multisegment support
- dna_scales, annotations on all the segments,
- Generated new examples.
- On plot_gene_maps, it is now possible to add automatic scale to any or
- It is possible (and recommended) to apply "global" color scheme at the
time of plotting (and not when parsing comparisons).
- 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