amp_timeseries: Abundance timeseries

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Abundance timeseries

Description

Generates a timeseries plot showing relative read abundances over time.

Usage

amp_timeseries(
  data,
  time_variable = NULL,
  group_by = NULL,
  tax_aggregate = "OTU",
  tax_add = NULL,
  tax_show = 5,
  tax_class = NULL,
  tax_empty = "best",
  split = FALSE,
  scales = "free_y",
  normalise = TRUE,
  plotly = FALSE,
  ...
)

amp_time_series(
  data,
  time_variable = NULL,
  group_by = NULL,
  tax_aggregate = "OTU",
  tax_add = NULL,
  tax_show = 5,
  tax_class = NULL,
  tax_empty = "best",
  split = FALSE,
  scales = "free_y",
  normalise = TRUE,
  plotly = FALSE,
  ...
)

Arguments

data	(required) Data list as loaded with amp_load.
time_variable	(required) The name of the column in the metadata containing the time variables, e.g. "Date". Must be directly compatible with as_date and preferably of the form "yyyy-mm-dd" or "%Y-%m-%d".
group_by	Group the samples by a variable in the metadata.
tax_aggregate	The taxonomic level to aggregate the OTUs. (default: "OTU")
tax_add	Additional taxonomic level(s) to display, e.g. "Phylum". (default: "none")
tax_show	The number of taxa to show, or a vector of taxa names. (default: 6)
tax_class	Converts a specific phylum to class level instead, e.g. "p__Proteobacteria".
tax_empty	How to show OTUs without taxonomic information. One of the following: "remove": Remove OTUs without taxonomic information. "best": (default) Use the best classification possible. "OTU": Display the OTU name.
split	Split the plot into subplots of each taxa. (default: FALSE)
scales	If split = TRUE, should the axis scales of each subplot be fixed (fixed), free ("free"), or free in one dimension ("free_x" or "free_y")? (default: "fixed")
normalise	(logical) Transform the OTU read counts to be in percent per sample. (default: TRUE)
plotly	(logical) Returns an interactive plot instead. (default: FALSE)
...	Additional arguments passed to as_date to make the time_variable compatible with the timeseries plot, fx the format or tz arguments, see ?as_date.

Value

A ggplot2 object.

Preserving relative abundances in a subset of larger data

See ?amp_filter_samples or the ampvis2 FAQ.

Author(s)

Julie Klessner Thun Pedersen [e-mail]

Kasper Skytte Andersen [e-mail]

See Also

amp_load

Examples

# Load example data
data("AalborgWWTPs")

# Timeseries of the 5 most abundant OTUs based on the "Date" column
amp_timeseries(AalborgWWTPs,
  time_variable = "Date",
  tax_aggregate = "OTU"
)

# As the above warning suggests, there are more than one sample per date in the data,
# in this case one from Aalborg East and one from Aalborg West. The average of the
# two samples is then shown per date. In such case it is then recommended to either
# subset the data, or group the samples by setting group_by = "" and split by tax_aggregate
# by setting split = TRUE:
amp_timeseries(AalborgWWTPs,
  time_variable = "Date",
  group_by = "Plant",
  split = TRUE,
  scales = "free_y",
  tax_show = 9,
  tax_aggregate = "Genus",
  tax_add = "Phylum"
)

MadsAlbertsen/ampvis2 documentation built on Jan. 28, 2024, 7:12 a.m.