plot_interaction_heatmap: Plot heatmap over all pairwise (MAP) correlations between...

In kimberlyroche/ROL: What the package does (short line)

Description

Plot heatmap over all pairwise (MAP) correlations between microbes at designated taxonomic level

Usage

plot_interaction_heatmap(
  tax_level = "ASV",
  logratio = "alr",
  Sigmas = NULL,
  DLM = FALSE,
  cluster = TRUE,
  taxon_idx = NULL,
  show_plot = FALSE,
  return_matrix = FALSE
)

Arguments

tax_level	taxonomic level at which to agglomerate data
logratio	logratio representation to use (e.g. "alr", "ilr", "clr")
Sigmas	optional list (indexed by host short name) of MAP estimates of microbial covariance; if not provided, this will be loaded
DLM	if TRUE, looks for DLM model fits instead of GP model fits
cluster	optional flag to hierarchically cluster across hosts and interactions
taxon_idx	optional logratio coordinate to render correlations against; if NULL, render all pairwise correlations
show_plot	optional flag to show() plot in addition to rendering it to a file
return_matrix	optional flag to return host x interaction correlation value matrix

Value

NULL or heatmap matrix

Examples

Sigmas <- load_MAP_estimates(tax_level = "ASV", DLM = TRUE, logratio = "clr")
plot_interaction_heatmap(tax_level = "ASV", logratio = "clr", Sigmas = Sigmas)

kimberlyroche/ROL documentation built on Dec. 10, 2020, 2:18 a.m.