correlation_plots: Get Multiple Correlation Plots

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

This function allows the user to create a list of multiple correlation plots.

Usage

correlation_plots(obj, primary_ranks, secondary_ranks = TRUE, ...)

Arguments

obj	An object to be converted to a Taxmap object with create_taxmap.
primary_ranks	A vector of primary ranks used to label the points.
secondary_ranks	The secondary rank used to color the points. Can be an integer specifying the number of supertaxon ranks above the primary rank or the name of a supertaxon rank. Default: TRUE
...	An optional list of parameters to use in the correlation_plot function.

Details

This function makes it easier to generate multiple correlation plots at once.

Value

A list object containing correlation plots. A pairwise comparison returns a nested list.

See Also

Other Visualizations: alpha_diversity_plot, correlation_data, correlation_plot, heat_tree_parameters, heat_tree_plots, ordination_plots, ordination_plot, plot_limits, save_alpha_diversity_plots, save_correlation_plots, save_heat_tree_plots, save_ordination_plots, save_stacked_barplots, stacked_barplots, stacked_barplot, top_coefficients_barplot

Examples

## Not run: 
if(interactive()){
# This example uses data that are no longer available in the MicrobiomeR package,
# however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
library(MicrobiomeR)
analyzed_silva <- as_MicrobiomeR_format(MicrobiomeR::raw_silva_2, "analyzed_format")
corr_plots <- correlation_plots(analyzed_silva, primary_ranks = c("Phylum", "Class", "Order"),
                      secondary_ranks = c("Phylum", "Class", "Order", "Family", "Genus"))
# Show a plot
corr_plots$Class$Phylum
 }

## End(Not run)

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.