plotBars

plotBars

R Documentation

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")