plotTaxonomy {SQMtools}

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 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")