networks_plot: networks_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

networks_plot

Description

Constructs and plots co-occurrence networks based on specific occurrence frequency (pre_threshold), permutation number (permutation), fdr threshold (fdr_threshold), association threshold (cor_threshold) with propr, sparcc and cclasso.

Usage

networks_plot(
  otu,
  taxa,
  sample,
  pre_threshold,
  fdr_threshold,
  cor_threshold,
  permutation,
  propr,
  sparcc,
  cclasso,
  spieceasi,
  propr_col,
  sparcc_col,
  cclasso_col,
  spieceasi_col
)

Arguments

otu	a community count data matrix with samples in rows and OTUs/taxa in column,
taxa	a taxa information matrix. The rownames must match the OTU names (taxa_names) of the otu,
sample	a sample information data.frame. The rownames must match the sample names in the otu,
pre_threshold	occurrence frequency,
fdr_threshold	fdr threshold,
cor_threshold	association threshold,
permutation	permutation number of the association methods,
propr	a logical value indicating whether to run propr,
sparcc	a logical value indicating whether to run sparcc,
cclasso	a logical value indicating whether to run cclasso,
spieceasi	a logical value indicating whether to run spieceasi,
propr_col	the color of propr network,
sparcc_col	the color of sparcc network,
cclasso_col	the color of cclasso network,
spieceasi_col	the color of spieceasi network,

Details

Constructs and plots networks based on specific occurrence frequency (pre_threshold), permutation number (permutation), fdr threshold (fdr_threshold), association threshold (cor_threshold) with propr, sparcc and cclasso.

Value

Co-occurrence network plots showing the relationship between otu.

Examples

 networks_plot(otu, taxa, sample, pre_threshold=0.5, fdr_threshold=0.1, cor_threshold=0.6, permutation=100, propr=TRUE, sparcc=TRUE, cclasso=TRUE, spieceasi=TRUE, propr_col='darkcyan', sparcc_col='firebrick3', cclasso_col='goldenrod3', spieceasi_col = 'dodgerblue3')

lindan1128/coreMicrobiome documentation built on May 5, 2022, 8:24 p.m.