plot_abundance: Area and bar plots of sample-level relative abundance at...

In waldronlab/nychanesmicrobiome: Analysis of the NYC-HANES Microbiome Specimens

Area and bar plots of sample-level relative abundance at specified taxonomic levels

Description

Area and bar plots of sample-level relative abundance at specified taxonomic levels

Usage

plot_abundance(
  pseq,
  top_n = 8,
  taxrank = "Phylum",
  prop_of = "top_n",
  type = "area",
  orderby_OTU,
  PALETTE
)

plot_abundance_by(
  pseq,
  brewerpal = "Set1",
  by,
  type = c("area", "bar"),
  ttle = paste0("Relative phylum abundances by ", by)
)

Arguments

pseq	An object of class phyloseq
top_n	Integer. Number of taxonomic groups to display, sorted by relative abundance
taxrank	Character. Taxonomic rank to display. Should be a column name of the taxa_table in pseq.
prop_of	Character. Either "top_n" or "total". Indicates whether heights of area/bars should represent the proportion out of the displayed taxonomic groups, or the out of the total.
type	Character. Either area or bar, specifying which type of plot. Area displays all samples left to right, whereas bars give mean abundances.
orderby_OTU	Character (optional). The OTU name (i.e. rowname in otu_table) whose relative abundance you would like to sort by. This is what creates the visual gradient from left to right of, say, Firmicutes.
PALETTE	Character of same length top_n of palette for area or bar chart.
brewerpal	Character. Name of RColorBrewer palette to use.
by	Character. Variable in sample_data to stratify plots by.
ttle	Character. Plot title.

waldronlab/nychanesmicrobiome documentation built on April 21, 2024, 8:52 a.m.