plotBars {SQMtools}

Plot a barplot using ggplot2

Description

Plot a ggplot2 barplot from a matrix or data frame. The data should be in tabular format (e.g. features in rows and samples in columns).

Usage

plotBars(
  data,
  label_x = "Samples",
  label_y = "Abundances",
  label_fill = "Features",
  color = NULL,
  base_size = 11,
  max_scale_value = NULL,
  metadata_groups = NULL
)

Arguments

data

Numeric matrix or data frame.

label_x

character Label for the x axis (default "Samples").

label_y

character Label for the y axis (default "Abundances").

label_fill

character Label for color categories (default "Features").

color

Vector with custom colors for the different features. If empty, the default ggplot2 palette will be used (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; plotHeatmap for plotting a heatmap with arbitrary data; mostAbundant for selecting the most abundant rows in a dataframe or matrix.

Examples

data(Hadza)
sk = Hadza$taxa$superkingdom$abund
plotBars(sk, label_y = "Raw reads", label_fill = "Superkingdom")