NEW FEATURES
- Added a
NEWS.mdfile to track changes to the package.
NEW FEATURES
- Replaced distance measure for clustering of phylogenomic profiles: from vegan::vegdist to labdsv::dsvdis
NEW FEATURES
-
Added functions fasta2AAStringSetlist and gff2GRangesList to help users read multiple FASTA and GFF/GTF files as list of AAStringSet and GRangesList, respectively.
-
Updated vignette to instruct users on how to load FASTA and GFF/GTF files to the R session.
NEW FEATURES
-
Ward's clustering of synteny clusters is now performed prior to plotting in
plot_profiles(), not inphylogenomic_profile(). As a consequence,phylogenomic_profile()now returns only a matrix of profiles, not a list containing the matrix and an hclust object. -
Added an option to handle names in vector cluster_species as new names for display in the heatmap. This way, species abbreviations can be easily replaced with species' full names to make plots look better.
-
Added parameters dist_function and dist_params to allow users to specify function and parameters to calculate the distance matrix that will be passed to Ward's clustering.
NEW FEATURES
-
Added parameters clust_function and clust_params in
cluster_network()to let users pass any igraph::cluster_* function to cluster the synteny network. -
Added parameters clust_function and clust_params in
plot_profiles()to let users have more control on the method used to cluster the distance matrix (columns in phylogenomic profiles). -
Updated vignette to reflect the changes mentioned above and included an FAQ item with instructions on how to update the R PATH variable.
BUG FIXES
- Tidy evaluation with aes_() was deprecated in ggplot 3.0.0, and testthat now returns warnings for it. Replaced aes_() with aes() and .data from the rlang package.