plotBins

plotBins

R Documentation

Barplot of the most abundant bins in a SQM object

Description

This function selects the most abundant bins across all samples in a SQM object and represents their abundances in a barplot. It can also plot their aggregated abundances at higher taxonomic ranks. Alternatively, a custom set of bins/taxa can be represented.

Usage

plotBins(
  SQM,
  rank = "bin",
  count = "percent",
  N = 15,
  tax_source = "bins",
  bins = NULL,
  tax = NULL,
  others = TRUE,
  samples = NULL,
  ignore_unmapped = FALSE,
  ignore_nobin = FALSE,
  no_partial_classifications = FALSE,
  rescale = FALSE,
  color = NULL,
  base_size = 11,
  max_scale_value = NULL,
  metadata_groups = NULL
)

Arguments

`SQM`	A SQM object.
`rank`	Taxonomic rank to plot (default `bin`).
`count`	character. Either `"abund"` for raw abundances, `"percent"` for percentages, `"cov"` for coverages, or `"cpm"` for coverages per million reads (default `"percent"`).
`N`	integer Plot the `N` most abundant bins (default `15`).
`tax_source`	character. Source of taxonomic annotations, can be `"bins"` (GTDB bin taxonomy if available, SQM bin taxonomy otherwise), `"bins_gtdb"` (GTDB bin taxonomy) or `"bins_sqm"` (SQM bin taxonomy) (default: `"bins"`.
`bins`	character. Custom bins/taxa to plot. If provided, it will override `N` (default `NULL`).
`tax`	character. Custom bins/taxa to plot. If provided, it will override `N` and `bins` (default `NULL`).
`others`	logical. Collapse the abundances of least abundant bins, 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`).
`ignore_unmapped`	logical. Don’t include unmapped reads in the plot (default `FALSE`).
`ignore_nobin`	logical. Don’t include reads which are not in a bin 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.

See Also

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

Examples

data(Hadza)
# Bins distribution.
plotBins(Hadza)
# Aggregated bin taxonomy
plotBins(Hadza, rank = 'order')