plot_core: Visualize OTU Core

In microbiome: Microbiome Analytics

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 [e-mail]

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(dietswap)
p <- plot_core(transform(dietswap, "compositional"),
  prevalences=seq(0.1, 1, .1), detections=seq(0.01, 1, length = 10))

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