plot_dendrogram: Generate a dendrogram based on a dissimilarity matrix

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Generate a dendrogram based on a dissimilarity matrix

Description

Generating a dendrogram can be useful for visualizing similarities and differences in community compositions among samples.

Usage

plot_dendrogram(dm, metadata_map, labels, color_by, method = "complete", ...)

Arguments

dm	Dissimilarity matrix.
metadata_map	The metadata mapping dataframe. Typically, input$map_loaded.
labels	The metadata mapping dataframe column name representing the intended leaf labels.
color_by	[OPTIONAL] The metadata mapping dataframe column name representing the intended leaf label colors.
method	The clustering method to use when creating the dendrogram.
...	Other parameters passed on to geom_text

Examples

fvrar = single_rarefy(fruits_veggies, 100)
dm = calc_dm(fvrar$data_loaded)
plot_dendrogram(
  dm, metadata_map = fvrar$map_loaded, labels = 'Sample_type',
  color_by = 'Farm_type'
)

leffj/mctoolsr documentation built on Aug. 5, 2022, 1:27 a.m.