plotTaxonomy

plotTaxonomy

R Documentation

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 Bacteroidota” 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.