Description Usage Arguments Details Value Author(s) References Examples
Show all samples of a microbiota collection, colored by specific factor levels (x axis) and signal (y axis).
1 | plot_atlas(pseq, x, y, ncol = 2)
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pseq |
phyloseq object |
x |
Sorting variable for X axis and sample coloring |
y |
Signal variable for Y axis |
ncol |
Number of legend columns. |
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).
ggplot object
Leo Lahti leo.lahti@iki.fi
See citation('microbiome'); Visualization inspired by Kilpinen et al. 2008, Genome Biology 9:R139. DOI: 10.1186/gb-2008-9-9-r139
1 2 3 | data(atlas1006)
p <- plot_atlas(atlas1006, 'DNA_extraction_method', 'diversity')
p <- plot_atlas(atlas1006, 'DNA_extraction_method', 'Bifidobacterium')
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