NEWS
chem16S 1.1.0 (2024-07-01)
- Change default reference database to GTDB version 214.
- Normalize file names in RefDB/RefSeq_206 and RefDB/GTDB_214 for easier
programmatic access.
- Add 'xvar' and 'yvar' arguments to plot_metrics().
- Add 'Domain' as an allowed rank in ps_taxacounts().
- Move calc_metrics() and add_hull() to the canprot package, which is now
imported by chem16S.
- A single 'metrics' argument replaces 'x' and 'y' in plot_ps_metrics2().
chem16S 1.0.0 (2023-07-17)
- Add functions for integration with phyloseq: ps_taxacounts(), ps_metrics(),
plot_ps_metrics(), and plot_ps_metrics2().
- Add vignettes: *Chemical metrics of reference proteomes*, *Integration of
chem16S with phyloseq*, and *Plotting two chemical metrics*.
- Change default reference database from RefSeq to GTDB.
- Add metrics: nO2, GRAVY, pI, MW, length, H/C, N/C, O/C, and S/C.
- Rename readRDP() to read_RDP(), getmetrics() to get_metrics(), plotmet() to
plot_metrics(), and other analogous changes to function names.
- First release on CRAN.
chem16S 0.1.3
- Add 'pt.open.col' argument to plotmet() for border color of open plot symbols.
- Add 'xlab' and 'ylab' arguments to plotmet().
chem16S 0.1.2
- Add reference proteomes for taxa based on the Genome Taxonomy Database (GTDB).
- Add 'return_AA' argument to getmetrics() to return amino acid composition.
- Add 'zero_AA' argument to getmetrics() to specify amino acids with
abundances set to zero for calculating chemical metrics.
chem16S 0.1.1
- Add 'cex' argument to plotmet().
- Don't drop dimensions in readRDP().
- Change "estimated community proteomes" to "community reference proteomes".
chem16S 0.1.0