NEWS

syntenet 1.3.5

NEW FEATURES

Added function run_last() to run alternative BLAST search. Vignette was updated accordingly.

BUG FIXES

BUG FIXES

Strand information is now preserved in the output of process_input() (for users who want to plot synteny).

NEW FEATURES

Added function collapse_protein_ids() to replace protein IDs in sequence names (equivalent to FASTA headers) with gene IDs. If there are multiple protein for the same gene, onlt the longest is kept. Vignette was updated accordingly.

BUG FIXES

Added a check for which IQ-TREE version is installed. If IQ-TREE2 is installed (and not IQ-TREE), arguments and call are modified accordingly, because IQ-TREE developers changed some parameters (e.g., -bb is now -B).

NEW FEATURES

Added a parameter as to parse_collinearity() that allows the extraction on synteny block information from .collinearity files. The vignette was updated accordingly.

BUG FIXES

Fixed species ID retrieval by adding an exported function named create_species_id_table() that correctly creates unique species IDs (3-5 characters), even when the first 5 characters are equal.
intraspecies_synteny() and interspecies_synteny() (originally unexported) now take the same output of process_input(), which makes them consistent with the entire package.

NEW FEATURES

To make it easier for users who want to run DIAMOND from the command line, I added the functions export_sequences() and read_diamond(), which write processed sequences to FASTA files and read the DIAMOND output, respectively. An example code on how to run DIAMOND from the command line has been added to the vignette.
Included a section in the vignette on how to use syntenet as a synteny detection program (i.e., to find synteny within a single genome or between two genomes).

BUG FIXES

Replaced sprintf calls with snprintf calls in C++ code to address warnings in the devel branch of Bioc

UPDATES

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.

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.

NEW FEATURES

Ward's clustering of synteny clusters is now performed prior to plotting in plot_profiles(), not in phylogenomic_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 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

Replaced distance measure for clustering of phylogenomic profiles: from vegan::vegdist to labdsv::dsvdis

NEW FEATURES