doc_elements.txt

#' @param phyloseq_obj A \code{\link[phyloseq]{phyloseq-class}} object.
#' @param classification The level of taxonomy to examine. Must be a column name
#' from the tax_table of the phyloseq_object.
#' \code{\link[phyloseq:tax_table]{tax_table}}.
#' @param treatment Column name as a string, or vector of strings, from the
#' \code{\link[phyloseq:sample_data]{sample_data}}.
#' @param subset A level within the \code{treatment}. Multiple levels can be 
#' given as a vector.
#' 
#' @param transformation Transformation to be used on the data. "none",
#' "relative_abundance", "log", "log10", "log1p", "log2", "asn", "atanh",
#' "boxcox", "exp", "identity", "logit", "probability", "probit",
#' "reciprocal", "reverse" and "sqrt"
#' 
#' @param colors This can be either a name of a color set from the
#' \link[=RColorBrewer]{RColorBrewer} package or a vector palette of R-accepted
#' colors. The default is an adaption of the palette from 
#' \url{https://www.nature.com/articles/nmeth.1618}
#' 
#' @param treatment_labels a vector of names to be used as labels for
#' treatments/facets, in the order they appear in the figure.
#' 
#' @param sample_labels a vector of names to be used as labels for Samples, 
#' in the order they appear in the figure.
#' 
#' @param classification_labels a vector of names to be used as labels for the
#' taxonomic classifications, in the order they appear in the figure.
#' 
#' 
#' @param co_occurrence_table Table of the co-occurrence of taxa/genes in the
#' \code{phyloseq_obj}, computed using \code{\link{co_occurrence}}. If no
#' table is given, it will be computed with the \code{phyloseq_obj}, using the
#' given \code{treatment} and \code{p} = 0.05.
#' @param layout (optional) an `igraph` layout of the network, for 
#' reproducibility, can be created with \code{\link{network_layout_ps}}.
#' @param nodes_of_interest A vector of names of classes within the
#' \code{classification} to be labeled in the figure.
#' @param node_colors This can be either a name of a color set from the
#' \link[=RColorBrewer]{RColorBrewer} package or a vector palette of R-accepted
#' colors. The default is an adaption of the palette from 
#' \url{https://www.nature.com/articles/nmeth.1618}
#' @param negative_positive_colors colors to use for the edges to represent 
#' negative and positive correlations, as a vector c("negative", "positive").
#' @param cluster if \code{TRUE}, will use igraph's
#' \code{\link[igraph:cluster_fast_greedy]{cluster_fast_greedy}} method.
#' Alternatively, you may pass a vector of cluster assignments with order
#' corresponding to the order of the \code{taxa_names} in the
#' \code{phyloseq_obj}.
#' @param cluster_colors This can be either a name of a color set from the
#' \link[=RColorBrewer]{RColorBrewer} package or a vector palette of R-accepted
#' colors. The default is an adaption of the palette from 
#' \url{https://www.nature.com/articles/nmeth.1618}
#' @param buffer Amount of space beyond the points to extend cluster ellipses.