plot_atlas: Visualize Samples of a Microbiota Atlas
In microbiome/microbiome: Microbiome Analytics

plot_atlas

R Documentation

Visualize Samples of a Microbiota Atlas

Description

Show all samples of a microbiota collection, colored by specific factor levels (x axis) and signal (y axis).

Usage

plot_atlas(pseq, x, y, ncol = 2)

Arguments

`pseq`	phyloseq object
`x`	Sorting variable for X axis and sample coloring
`y`	Signal variable for Y axis
`ncol`	Number of legend columns.

Details

Arranges the samples based on the given grouping factor (x), and plots the signal (y) on the Y axis. The samples are randomly ordered within each factor level. The factor levels are ordered by standard deviation of the signal (y axis).

Value

ggplot object

Author(s)

Leo Lahti leo.lahti@iki.fi

References

See citation('microbiome'); Visualization inspired by Kilpinen et al. 2008, Genome Biology 9:R139. DOI: 10.1186/gb-2008-9-9-r139

Examples

data(atlas1006)
p <- plot_atlas(atlas1006, 'DNA_extraction_method', 'diversity')
p <- plot_atlas(atlas1006, 'DNA_extraction_method', 'Bifidobacterium')

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.