plotBins {SQMtools}

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 or a SQMlite 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

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

Examples

data(Hadza)
# Bins distribution.
plotBins(Hadza)