save_alpha_diversity_plots: Save Alpha Diversity Plots

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

This function saves alpha diversity plots stored in a list object to an output folder.

Usage

save_alpha_diversity_plots(alpha_div_plots, format = "tiff",
  start_path = "output", ...)

Arguments

alpha_div_plots	A named list of alpha diversity plots.
format	The format of the output image. Default: 'tiff'
start_path	The starting path of the output directory. Default: 'output'
...	An optional list of parameters to use in the output_dir function.

Details

This function creates an appropriate output directory, where it saves publication ready plots.

Value

An output directory that contains alpha diversity plots.

See Also

output_dir

ggsave

Other Visualizations: alpha_diversity_plot, correlation_data, correlation_plots, correlation_plot, heat_tree_parameters, heat_tree_plots, ordination_plots, ordination_plot, plot_limits, 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")
  alpha_div_plots <- alpha_diversity_plots(analyzed_silva)
  # Save to \emph{./output/alpha_diversity} folder.
  save_alpha_diversity_plot(alpha_div_plots)
}

## End(Not run)

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