networks_shared_ne_plot: networks_shared_ne_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

networks_shared_ne_plot

Description

Constructs the co-occurrence networks and calculates the common/shared nodes/edges among networks from different methods and visualization.

Usage

networks_shared_ne_plot(
  otu,
  taxa,
  sample,
  pre_threshold,
  fdr_threshold,
  cor_threshold,
  permutation,
  propr = TRUE,
  sparcc = TRUE,
  cclasso = TRUE,
  propr_col,
  sparcc_col,
  cclasso_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,
propr_col	the color of the properties of propr network,
sparcc_col	the color of the properties of sparcc network,
cclasso_col	the color of the properties of cclasso network,

Details

Constructs the co-occurrence networks and calculates the common/shared nodes/edges among networks from different methods and visualization.

Value

Upset plots showing the common/shared nodes/edges between networks.

Examples

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

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