orp16S_util {JMDplots}

R Documentation

Plotting functions for orp16S paper

Description

Make plots of Z_C vs Eh7 and Z_C vs abundance of Most Abundant Mapped Taxon.

Usage

  plotEZ(study, lineage = NULL, mincount = 100, pch = NULL, col = NULL,
    add = FALSE, type = "p", groupby = NULL, groups = NULL, legend.x = "topleft",
    show = c("lm", "points"), col.line = "gray62", lwd = 1, cex = 1,
    title.line = NA, dxlim = c(0, 0), dylim = c(0, 0), size = NULL,
    slope.legend = "title", ylim = NULL, ylab = cplab$Zc)
  plotMA(study, lineage = NULL, mincount = 100, pch = NULL, col = NULL,
    groupby = NULL, groups = NULL, legend.x = "topright")

Arguments

study	character, study key
lineage	character, regular expression for filtering lineages, or the keyword ‘⁠two⁠’
mincount	integer, samples with less than this number of RDP classifications are excluded
pch	point symbol
col	color(s) for points
add	logical, add to existing plot?
type	plot type, as in plot.default
groupby	character, column name for grouping samples
groups	character, names of sample groups
legend.x	legend placement (x argument for legend)
show	character, show these plot elements
col.line	line color (linear fit)
lwd	line width
cex	character expansion
title.line	numeric, placement of title (use NULL to omit title)
dxlim	numeric, adjustment to x-axis limits
dylim	numeric, adjustment to y-axis limits
size	numeric, number of randomly selected samples (see getmdat_orp16S)
slope.legend	character, legend placement for slope (‘⁠title⁠’ for above the plot, NULL for no slope legend)
ylim	numeric, y-axis limits (overrides dylim)
ylab	y-axis label

Details

plotEZ is used to make Z_C-Eh7 scatterplots for a single study. By default, Z_C is calculated for estimated proteomes using all bacterial and archaeal sequences. Set lineage to ‘⁠Bacteria⁠’ or ‘⁠Archaea⁠’ to make one plot, or to ‘⁠two⁠’ to make two plots (one for each domain). The latter option is used in orp16S_S1 for some of the plots in Figure S1 in the paper.

plotMA plots Z_C vs the percent abundance of most abundant mapped taxon (MAMT). The plot title shows the percentages of MAMT and MAUT (most abundant unmapped taxon).

Value

plotEZ returns a list with elements study, envirotype (environment type), lineage, metadata (output of getmdat_orp16S), and EZdat. EZdat is a data frame with one row per sample and columns for study, envirotype, lineage, sample (sample name), Run (SRA run accession or other database ID), Eh, Eh7, and Zc. If groupby and groups are given, EZdat additionally contains columns groupby and group. If show includes ‘⁠lm⁠’, the output additionally contains EZlm (the result of lm(Zc ~ Eh7, EZdat)), Eh7lim (range of Eh7 values), and Zcpred (fitted Z_C values for this Eh7 range).

See Also

orp16S

Examples

plotEZ("MLL+19", "Bacteria", groupby = "Type", groups = c("Upland", "Paddy", "Sediment"))

plotMA("LMBA21", "Archaea")

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