plot_starburst {JMDplots}

R Documentation

Starburst plot for parent and children taxa

Description

Plots chemical metrics of reference proteomes for parent taxa and their children. Lines are drawn from each parent to all of its children, creating a starburst pattern.

Usage

  plot_starburst(taxa = c("Bacteria", "Archaea"), metrics = c("Zc", "nH2O"),
    refdb = "RefSeq", remove_species_20000 = TRUE, terminal_H2O = 0,
    xlim = NULL, ylim = NULL, pch = NULL, col = seq_along(taxa), lcol = NULL,
    lwd = rep(1, length(taxa)), hline = NULL, legend.x = NA, identify = FALSE)

Arguments

taxa	character, names of parent taxa
metrics	character, two chemical metrics (see metrics)
refdb	character, reference database (‘⁠RefSeq⁠’ or ‘⁠GTDB⁠’)
remove_species_20000	logical, remove species with > 20000 sequences?
terminal_H2O	numeric, how to count terminal groups for calculation of nH2O
xlim	numeric, x axis limits
ylim	numeric, y axis limits
pch	plotting symbols
col	colors for plotting symbols and lines
lcol	colors for lines; default corresponds to adjustcolor(col, alpha.f = 0.5)
lwd	line widths
hline	numeric, coordinates of horizontal lines to add
legend.x	position of legend; default is to draw no legend
identify	logical, run identify for interactive identification of points?

Details

plot_starburst plots the indicated chemical metrics of the reference proteome for each taxon in taxa. Lines are drawn from each taxon to all of their children at the next lowest taxonomic rank. Use refdb to change the reference database; the default retrieves amino acid compositions and taxonomic names from the files extdata/RefDB/RefSeq/genome_AA.csv.xz and extdata/RefDB/RefSeq/taxonomy.csv.xz. remove_species_20000 removes all species with more than 20000 reference sequences (applies only for refdb == "RefSeq").

terminal_H2O and hline are provided to enable reproduction of the published figure for geo16S1. In that figure, the n_H2O values include the contribution of terminal groups (i.e., 1 H₂O per protein, divided by the length of the protein). Subsequently, in other publications, the contribution of terminal groups to n_H2O has been suppressed.

Examples

# Default plot for Bacteria and Archaea (parents)
# with lines drawn to phyla in each domain (children)
plot_starburst(legend.x = "bottomleft")

---