timeseries: Timeseries

In julieklessner/timeseries:

Description

This function allows you plot relative abundance reads over time in a timeseries plot.

Usage

timeseries(data, time, tax.aggregate = "Phylum", tax.add = NULL,
  tax.class = NULL, tax.empty = "best", plot.x.label = "Time",
  plot.y.label = "Abundance", plot.legend.title = "Sample",
  plot.theme = "normal", plot.layout = "dygraph")

Arguments

data	(required) A phyloseq object.
time	(required) The name of the column containing the time variables, e.g. "Date".
tax.aggregate	The taxonomic level that the data should be aggregated to (default: "Phylum")
tax.add	Additional taxonomic levels to display for each entry, e.g. "Phylum" (default: "none").
tax.class	Converts a specific phyla to class level instead, e.g. "p__Proteobacteria" (default: "none) .
tax.empty	Either "remove" OTUs without taxonomic information, add "best" classification or add the "OTU" name (default: "best").
plot.x.label	Label on x-axis (default: "Time").
plot.y.label	Label on y-axis (default: "Abundance").
plot.legend.title	Label on ggplot legend. (default: "Sample").
plot.theme	Chose different standard layouts choose from "normal" or "clean" (default: "normal").
plot.layout	Either "ggplot" or "dygraph" (default: "dygraph").
group	A variable from the associated sample data to group samples by (default: "Samples").

Author(s)

Julie Klessner Thun Pedersen [e-mail]

julieklessner/timeseries documentation built on May 20, 2019, 4:22 a.m.