Generate a Heatmap of Relative Abundance

This function creates a heatmap of relative abundance data from a phyloseq object (or similar data frame) at the genus level. It calculates the relative abundance of each taxon per sample and groups taxa with low relative abundance (below a defined threshold) into an "Other" category. The heatmap is then facetted based on additional sample metadata if available and saved as a PDF.

Usage

heatmap(
  physeq = rarefied_genus_psmelt,
  ntaxa = NULL,
  norm_method = NULL,
  taxrank = c("Phylum", "Class", "Order", "Family", "Genus"),
  date_factor = NULL
)

Arguments

physeq

A phyloseq object containing normalized genus-level data. The default is rarefied_genus_psmelt.

ntaxa

An integer specifying the maximum number of taxa to display individually. Taxa below the threshold are grouped into "Other". If NULL, ntaxa is set to 23.

norm_method

A character string specifying the normalization method. If NULL, the function uses the provided physeq directly. If set to "fcm" or "qpcr", the function extracts the corresponding psmelt_copy_number_corrected_ data based on the taxonomic rank.

taxrank

A character string indicating the taxonomic rank to use for grouping taxa. The default is "Genus".

Value

A ggplot object representing the heatmap of relative abundance.

Details

The function performs the following steps:

1. Sets up project folder paths for figures and output data.

2. Extracts and processes the input data to compute the relative abundance (in percentage) of each taxon per sample.

3. Groups taxa with a mean relative abundance below a defined cutoff into an "Other" category.

4. Optionally orders the data by Sample_Date if that factor is present in the metadata.

5. Creates a base heatmap using ggplot2, with samples on the x-axis and taxa on the y-axis. The fill color reflects the relative abundance, and text labels are added for values exceeding a threshold.

6. If more than one na_type is present (e.g., both DNA and RNA), separate heatmaps are generated for each and then combined.

7. Saves the final heatmap as a PDF file in the project's figures folder.

Examples

if (FALSE) { # \dontrun{
  # Generate a heatmap using default parameters
  heatmap_plot <- heatmap(physeq = rarefied_genus_psmelt)

  # Generate a heatmap with a specified number of taxa and a normalization method
  heatmap_plot <- heatmap(
    physeq = rarefied_genus_psmelt,
    ntaxa = 20,
    norm_method = "fcm",
    taxrank = c("Phylum", "Class", "Order", "Family", "Genus")
  )
} # }