plot_core {microbiome} | R Documentation

## Visualize OTU Core

### Description

Core visualization (2D).

### Usage

    plot_core(x, prevalences = seq(0.1, 1, 0.1), detections = 20,
      plot.type = "lineplot", colours = NULL, min.prevalence = NULL,
      taxa.order = NULL, horizontal = FALSE)

### Arguments

`x` | A `phyloseq` object or a core matrix
`prevalences` | a vector of prevalence percentages in [0,1]
`detections` | a vector of intensities around the data range, or a scalar indicating the number of intervals in the data range.
`plot.type` | Plot type ('lineplot' or 'heatmap')
`colours` | colours for the heatmap
`min.prevalence` | If minimum prevalence is set, then filter out those rows (taxa) and columns (detections) that never exceed this prevalence. This helps to zoom in on the actual core region of the heatmap. Only affects the plot.type='heatmap'.
`taxa.order` | Ordering of the taxa: a vector of names.
`horizontal` | Logical. Horizontal figure.

### Value

A list with three elements: the ggplot object and the data. The data has a different form for the lineplot and heatmap. Finally, the applied parameters are returned.

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')

### Examples

    data(atlas1006)
    pseq <- subset_samples(atlas1006, DNA_extraction_method == 'r')
    p <- plot_core(transform(pseq, "compositional"),
      prevalences=seq(0.1, 1, .1), detections=seq(0.01, 1, length = 10))

[Package microbiome version 1.0.2 Index]