Perform repeated rarefaction — repeated

This function performs repeated rarefaction on a phyloseq object, computes ordination, and generates a PCoA-based visualization. The same procedure is used from threshold_testing function when testing a range of thresholds.

Usage

repeated_rarefaction(
  input,
  repeats = 50,
  threshold = 250,
  colorb = "sample_id",
  group = "sample_id",
  cloud = TRUE,
  ellipse = FALSE,
  cores = 2,
  ...
)

Arguments

input: A phyloseq object.
repeats: An integer. The number of times to repeat rarefaction. A value of 1 means no repeats. If too few repeats are selected it would be not possible to draw an ellipse around the group.
threshold: An integer. The threshold value to use for rarefaction.
colorb: A string. Column name in sample_data(). Used to color sample points.
group: A string. Column name in sample_data(). Used to group the samples. The parameter is also used to draw an ellipse around the points.
cloud: A boolean. If TRUE, all the data points generated from repetitions are shown. Otherwise, only the median points of each sample repetition cloud are plotted.
ellipse: A boolean. If TRUE, confidence ellipses around sample groups are drawn.
cores: An integer. Number of cores to use for parallel processing.
...: Additional arguments are reserved to internal use.

Value

A list containing (While also showing the plot directly):

repeats: Number of repeats.
df_consensus_coordinates: A data frame with coordinates of the median points of the sample clouds.
df_all: A data frame of coordinates ordered by ordination number, along with metatata.
plot: a ggplot object.

Examples

library(Sibyl)
# Running this with cloud = TRUE and ellipse = TRUE will generate a plot 
# where the samples belonging to the same group will be colored similarly 
# and an ellipse will be drawn around the group.
repeated_rarefaction(adults, 
                     repeats = 10, 
                     threshold = 250, 
                     group = "location", 
                     colorb = "location", 
                     cloud = TRUE, 
                     ellipse = TRUE)

                     
# We can run the function to highlight the spread of the single sample clouds
# too, setting the groupb parameter to the sample_id.
repeated_rarefaction(adults, 
                     repeats = 10, 
                     threshold = 250, 
                     group = "sample_id", 
                     colorb = "location", 
                     cloud = TRUE, 
                     ellipse = TRUE)