plotTaxonomy: Barplot of the most abundant taxa in a SQM object

In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

Barplot of the most abundant taxa in a SQM object

Description

This function selects the most abundant taxa across all samples in a SQM object and represents their abundances in a barplot. Alternatively, a custom set of taxa can be represented.

Usage

plotTaxonomy(
  SQM,
  rank = "phylum",
  count = "percent",
  N = 15,
  tax = NULL,
  others = TRUE,
  samples = NULL,
  nocds = "treat_separately",
  ignore_unmapped = FALSE,
  ignore_unclassified = FALSE,
  no_partial_classifications = FALSE,
  rescale = FALSE,
  color = NULL,
  base_size = 11,
  max_scale_value = NULL,
  metadata_groups = NULL
)

Arguments

SQM	A SQM, SQMbunch or a SQMlite object.
rank	Taxonomic rank to plot (default phylum).
count	character. Either "percent" for percentages, or "abund" for raw abundances (default "percent").
N	integer Plot the N most abundant taxa (default 15).
tax	character. Custom taxa to plot. If provided, it will override N (default NULL).
others	logical. Collapse the abundances of least abundant taxa, and include the result in the plot (default TRUE).
samples	character. Character vector with the names of the samples to include in the plot. Can also be used to plot the samples in a custom order. If not provided, all samples will be plotted (default NULL).
nocds	character. Either "treat_separately" to treat reads annotated as No CDS separately, "treat_as_unclassified" to treat them as Unclassified or "ignore" to ignore them in the plot (default "treat_separately").
ignore_unmapped	logical. Don't include unmapped reads in the plot (default FALSE).
ignore_unclassified	logical. Don't include unclassified reads in the plot (default FALSE).
no_partial_classifications	logical. Treat reads not fully classified at the requested level (e.g. "Unclassified bacteroidetes" at the class level or below) as fully unclassified. This takes effect before ignore_unclassified, so if both are TRUE the plot will only contain fully classified contigs (default FALSE).
rescale	logical. Re-scale results to percentages (default FALSE).
color	Vector with custom colors for the different features. If empty, we will use our own hand-picked pallete if N<=15, and the default ggplot2 palette otherwise (default NULL).
base_size	numeric. Base font size (default 11).
max_scale_value	numeric. Maximum value to include in the y axis. By default it is handled automatically by ggplot2 (default NULL).
metadata_groups	list. Split the plot into groups defined by the user: list('G1' = c('sample1', sample2'), 'G2' = c('sample3', 'sample4')) default NULL).

Value

a ggplot2 plot object.

See Also

plotFunctions for plotting the most abundant functions of a SQM object; plotBars and plotHeatmap for plotting barplots or heatmaps with arbitrary data.

Examples

data(Hadza)
Hadza.amin = subsetFun(Hadza, "Amino acid metabolism")
# Taxonomic distribution of amino acid metabolism ORFs at the family level.
plotTaxonomy(Hadza.amin, "family")

SQMtools documentation built on April 3, 2025, 6:16 p.m.