plot_metrics: Plot chemical metrics of community reference proteomes

In chem16S: Chemical Metrics for Microbial Communities

Plot chemical metrics of community reference proteomes

Description

Functions to plot chemical metrics of community reference proteomes.

Usage

  plot_metrics(mdat,
    xvar = "Zc", yvar = "nH2O",
    xlim = NULL, ylim = NULL,
    xlab = chemlab(xvar), ylab = chemlab(yvar),
    plot.it = TRUE, add = FALSE, identify = FALSE,
    points = TRUE, lines = FALSE, title = TRUE,
    cex = 1, pt.open.col = 1, pch1 = 1, pch2 = 21,
    return = "data", extracolumn = NULL
  )

Arguments

mdat	list, output by get_metadata
xvar	character, name of x variable
yvar	character, name of y variable
xlim	numeric, x axis limits
ylim	numeric, y axis limits
xlab	x axis label
ylab	y axis label
plot.it	logical, make a plot?
add	logical, add to existing plot?
identify	logical, run identify for interactive identification of points?
points	logical, plot points?
lines	logical, plot lines?
title	character, plot title
cex	numeric, point size
pt.open.col	color of border for open point symbols (pch > 20)
pch1	numeric, symbol for samples in group 1
pch2	numeric, symbol for samples in group 2
return	character, indicates whether to return ‘⁠data⁠’ values or group ‘⁠means⁠’
extracolumn	character, the name of one or more extra columns (from get_metadata) to include in the output

Details

plot_metrics plots the values of \Zc and \nH2O (or other variables indicated by xvar and yvar) provided in mdat$metrics. Symbol shape and color (pch and col) are taken from mdat$metadata.

If pch1 and pch2 are provided, then samples are classified into two groups according to the value of mdat$metadata$pch. Mean values of the chemical metrics for each group are plotted with star-shaped symbols.

Value

For plot_metrics, a data frame with columns for study name and Run IDs (‘⁠name⁠’, ‘⁠Run⁠’), chemical metrics (taken from mdat$metrics), and symbols and colors for plotting points (‘⁠pch⁠’, ‘⁠col⁠’).

References

Herlemann, D. P. R., Lundin, D., Andersson, A. F., Labrenz, M. and Jürgens, K. (2016) Phylogenetic signals of salinity and season in bacterial community composition across the salinity gradient of the Baltic Sea. Front. Microbiol. 7, 1883. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3389/fmicb.2016.01883")}

Examples

# Make a plot for the Baltic Sea salinity gradient
# (data from Herlemann et al., 2016)
RDPfile <- system.file("extdata/RDP/HLA+16.tab.xz", package = "chem16S")
RDP <- read_RDP(RDPfile)
map <- map_taxa(RDP, refdb = "RefSeq_206")
metrics <- get_metrics(RDP, map, refdb = "RefSeq_206")
mdatfile <- system.file("extdata/metadata/HLA+16.csv", package = "chem16S")
mdat <- get_metadata(mdatfile, metrics)
pm <- plot_metrics(mdat)
# Add a legend
legend <- c("< 6 PSU", "6-20 PSU", "> 20 PSU")
pch <- c(24, 20, 21)
pt.bg <- c(3, NA, 4)
legend("bottomright", legend, pch = pch, col = 1, pt.bg = pt.bg, bg = "white")
# Classify samples with low and high salinity
ilo <- mdat$metadata$salinity < 6
ihi <- mdat$metadata$salinity > 20
# Add convex hulls
canprot::add_hull(pm$Zc[ilo], pm$nH2O[ilo],
  col = adjustcolor("green3", alpha.f = 0.3), border = NA)
canprot::add_hull(pm$Zc[ihi], pm$nH2O[ihi],
  col = adjustcolor("blue", alpha.f = 0.3), border = NA)

# Show points for all samples and larger star-shaped points
# for mean values of high- and low-salinity samples
plot_metrics(mdat, pch1 = 21, pch2 = 24)

# Plot nO2 instead of Zc
plot_metrics(mdat, xvar = "nO2")

# Make a plot for only Proteobacteria
RDP <- read_RDP(RDPfile, lineage = "Proteobacteria")
map <- map_taxa(RDP, refdb = "RefSeq_206")
metrics <- get_metrics(RDP, map, refdb = "RefSeq_206")
mdatfile <- system.file("extdata/metadata/HLA+16.csv", package = "chem16S")
mdat <- get_metadata(mdatfile, metrics)
mdat$metadata$name <- paste(mdat$metadata$name, "(Proteobacteria)")
plot_metrics(mdat)

chem16S documentation built on April 3, 2025, 10:47 p.m.