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Plot a Microbiome Heatmap

Source: R/plot_microbiome_visualization.R
plot_heatmap.Rd

Draw a heatmap of dominant taxa across samples.

Usage

plot_heatmap(
  object,
  taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  top_n = 20,
  relative = TRUE,
  cluster_samples = TRUE,
  cluster_taxa = TRUE,
  sample_label = "sample_id"
)

Arguments

object

A microbiome_dataset object.

taxonomic_rank

Taxonomic rank used for aggregation.

top_n

Number of taxa displayed.

relative

Whether to use relative abundance.

cluster_samples

Whether to cluster samples.

cluster_taxa

Whether to cluster taxa.

sample_label

Sample metadata column shown on the x axis.

Value

A ggplot object.

Examples

data("global_patterns", package = "microbiomedataset")

plot_heatmap(
  object = global_patterns,
  taxonomic_rank = "Phylum",
  top_n = 12,
  sample_label = "SampleType"
)