plotBins: Barplot of the most abundant bins in a SQM object

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

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. Alternatively, a custom set of bins can be represented.

Usage

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

Arguments

SQM	A SQM object.
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).
bins	character. Custom bins to plot. If provided, it will override N (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).
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)

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