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.
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
)a ggplot2 plot object.
A SQM or a SQMlite object.
Taxonomic rank to plot (default phylum).
character. Either "percent" for percentages, or "abund" for raw abundances (default "percent").
integer Plot the N most abundant taxa (default 15).
character. Custom taxa to plot. If provided, it will override N (default NULL).
logical. Collapse the abundances of least abundant taxa, and include the result in the plot (default TRUE).
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).
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").
logical. Don't include unmapped reads in the plot (default FALSE).
logical. Don't include unclassified reads in the plot (default FALSE).
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).
logical. Re-scale results to percentages (default FALSE).
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).
numeric. Base font size (default 11).
numeric. Maximum value to include in the y axis. By default it is handled automatically by ggplot2 (default NULL).
list. Split the plot into groups defined by the user: list('G1' = c('sample1', sample2'), 'G2' = c('sample3', 'sample4')) default NULL).
plotFunctions for plotting the most abundant functions of a SQM object; plotBars and plotHeatmap for plotting barplots or heatmaps with arbitrary data.
data(Hadza)
Hadza.amin = subsetFun(Hadza, "Amino acid metabolism")
# Taxonomic distribution of amino acid metabolism ORFs at the family level.
plotTaxonomy(Hadza.amin, "family")
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