network_ps: Create an igraph network object of the co-occurrence from a...

In schuyler-smith/phylosmith: Functions to help analyze data as phyloseq objects

Create an igraph network object of the co-occurrence from a phyloseq object. Function from the phylosmith-package.

Description

Create an igraph network object of the co-occurrence from a phyloseq object. This can be input into the co_occurrence_network function, or used for other network creating scripts. The purpose is to be able to create reproducible and comparable graphics.

Usage

network_ps(phyloseq_obj,
treatment = NULL, subset = NULL, co_occurrence_table = NULL, rho = 0.6)

Arguments

phyloseq_obj	A phyloseq-class object. It must contain sample_data()) with information about each sample, and it must contain tax_table()) with information about each taxa/gene.
treatment	Column name as a string or number in the sample_data. This can be a vector of multiple columns and they will be combined into a new column.
subset	A factor within the treatment. This will remove any samples that to not contain this factor. This can be a vector of multiple factors to subset on.
co_occurrence_table	Table of the co-occurrence of taxa/genes in the phyloseq_obj, computed using co_occurrence. If no table is given, it will be computed with the phyloseq_obj, using the given treatment and p = 0.05.
rho	numeric The rho-value cutoff. All returned co-occurrences will have a rho-value less than or equal to rho or less than or equal to -rho.

Value

igraph network object

Examples

network_ps(soil_column, treatment = c('Matrix', 'Treatment'),
subset = 'Soil Amended')

schuyler-smith/phylosmith documentation built on Feb. 6, 2025, 1:56 p.m.