plot_atlas {microbiome} | 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')

[Package microbiome version 1.2.1 Index]