ggrare: Make a rarefaction curve using ggplot2

In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses

Description

Make a rarefaction curve using ggplot2

Usage

ggrare(physeq_object, step = 10, label = NULL, color = NULL,
  plot = TRUE, parallel = FALSE, se = TRUE)

Arguments

physeq_object	A phyloseq class object, from which abundance data are extracted
step	Step Size for sample size in rarefaction curves
label	Default 'NULL'. Character string. The name of the variable to map to text labels on the plot. Similar to color option but for plotting text.
color	Default 'NULL'. Character string. The name of the variable to map to the colors in the plot. This can be a sample variables among the set returned by sample_variables(physeq_object) or taxonomic rank, among the set returned by rank_names(physeq_object)
plot	default 'TRUE'. Logical. Should the graph be plotted
parallel	default 'FALSE'. Logical. Should rarefaction be parallelized
se	default 'TRUE'. Logical. Should standard errors be calculated.

Examples

good_taxon_table <- data.frame(sum.taxonomy = c("a;b;c;d;f;u", "p;q;r;s;t;u"),
site_1 = c(0,1), site_2 = c(10, 20))
good_maps <- data.frame(site = c("site_1", "site_2"),
season = c("wet", "dry"), host = c("oak", "sage"))
physeq_object <- convert_anacapa_to_phyloseq(good_taxon_table, good_maps)
ggrare(physeq_object, step = 20, se = TRUE)

gauravsk/ranacapa documentation built on June 7, 2019, 4:03 a.m.