This function creates a rarefaction curve for a given phyloseq object and
saves the plot as a PDF.
Usage
rarefaction_curve(
physeq = resolved_tree_physeq,
color = NULL,
base_path = "./"
)
Arguments
- physeq
A phyloseq object containing the microbiome data.
This is the input object that the function processes.
- color
A character string specifying the column in the sample metadata to use for
coloring the samples. Default is NULL, which automatically sets the color
to "sample_or_control".
Value
The rarefaction curve plot object.
Details
This function first checks whether the sample_or_control column exists in the
sample metadata. It then generates a rarefaction curve using the amp_rarecurve
function and saves the plot as a PDF file in the specified directory.
Examples
rarefaction_curve(physeq = physeq)
#> Error in log_message(paste("Step 6: Creating rarefaction curve: creating rarefaction curve before cleaning on ASV level.", paste(projects, collapse = ", ")), log_file): could not find function "log_message"