plot_atlas: Visualize Samples of a Microbiota Atlas

Description Usage Arguments Details Value Author(s) References Examples

View source: R/plot_atlas.R

Description

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

Usage

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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

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

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.