Filter a phyloseq object to include only taxa that are present in the phylogenetic tree, or prune the tree to match the taxa in the phyloseq. Can also filter based on tree properties like tip labels matching a pattern.
Usage
filter_tree_pq(
physeq,
taxa = NULL,
pattern = NULL,
invert = FALSE,
clean_phyloseq_object = TRUE
)Arguments
- physeq
(phyloseq, required) A phyloseq object with a phy_tree slot.
- taxa
(character, optional) Character vector of taxa names to keep. If NULL, keeps all taxa that are present in both the OTU table and tree.
- pattern
(character, optional) A regular expression pattern to match against tip labels. Only tips matching the pattern are kept.
- invert
(logical, default FALSE) If TRUE and pattern is provided, keep tips that do NOT match the pattern.
- clean_phyloseq_object
if TRUE (default), the resulting phyloseq object is cleaned using
clean_pq()to remove empty taxa/samples.
Examples
library(MiscMetabar)
# Synchronize tree with OTU table (remove taxa not in tree)
# filter_tree_pq(physeq_with_tree)
# Keep only specific taxa in tree
# filter_tree_pq(physeq_with_tree, taxa = c("ASV1", "ASV2", "ASV3"))
# Filter by tip label pattern
# filter_tree_pq(physeq_with_tree, pattern = "^ASV")