phfnetworks: phfnetworks
In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

phfnetworks

R Documentation

phfnetworks

Description

Constructs a plot combining the phylogenetic tree, the heatmaps showing average occurrence frequency and average relative abundance of each taxa, and the co-occurrence networks from different methods.

Usage

phfnetworks(
  otu,
  taxa,
  sample,
  tree,
  functional_profile,
  propr = TRUE,
  sparcc = TRUE,
  cclasso = TRUE,
  cluster_method,
  pre_threshold,
  fdr_threshold,
  cor_threshold,
  permutation,
  nscore = "degree",
  hcol = "red",
  propr_col = "darkcyan",
  sparcc_col = "firebrick3",
  cclasso_col = "goldenrod3",
  ttip = 3,
  tlab = 2,
  hlab = 4,
  llab = 10,
  alab = 4,
  offset = 0.3,
  width = 1,
  mini_abun,
  threshold,
  sample_name,
  sample_group,
  mini_tpm,
  threshold_tpm,
  both_core_col,
  common_core_col,
  func_core_col,
  non_core_col,
  hub_col,
  non_hub_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,
`tree`	a phylogenetic tree. The tip labels must match the otu names in the otu,
`functional_profile`	a community count data matrix with samples in rows and OTUs/taxa in column,
`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,
`cluster_method`	module clustering methods, including cluster_walktrap, cluster_edge_betweenness, cluster_fast_greedy and cluster_spinglass,
`pre_threshold`	occurrence frequency,
`fdr_threshold`	fdr threshold,
`cor_threshold`	association threshold,
`permutation`	permutation number of the association methods,
`nscore`	the node-level property (degree, betweenness and closeness),
`hcol`	the color of heatmap,
`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,
`ttip`	the node size of the tree,
`tlab`	the font size of the tree tip label,
`hlab`	the font size of the heatmap label,
`llab`	the font size of the legend label,
`alab`	the font size of the title,
`offset`	the offset between each subfigure,
`width`	the width of each heatmap cell,
`mini_abun`	a value indicating whether the otu is present,
`threshold`	a value indicating the final percent increase in beta-diversity,
`sample_name`	the name of a column that containing the sample name,
`sample_group`	the name of a column that containing the sample type/group,
`mini_tpm`	a value indicating whether the function is present,
`threshold_tpm`	a value indicating the final percent increase in beta-diversity,
`both_core_col`	the color of the both-core nodes in the tree
`common_core_col`	the color of the common-core nodes in the tree
`func_core_col`	the color of the functional-core nodes in the tree
`non_core_col`	the color of the non-core nodes in the tree
`hub_col`	the color of the hubs in the network
`non_hub_col`	the color of the non-hubs in the network

Details

Value

Combined plot showing the phylogenetic tree, the heatmap and co-occurrence networks.

Examples

 phfnetworks(otu, taxa, sample, tree, functional_profile, propr = TRUE, sparcc = TRUE, cclasso = TRUE, cluster_method="cluster_walktrap", pre_threshold, fdr_threshold, cor_threshold, permutation, nscore = 'degree', hcol = 'red', propr_col = 'darkcyan', sparcc_col = 'firebrick3', cclasso_col = 'goldenrod3', ttip = 3, tlab = 2, hlab = 4, llab = 4, offset = 0.3, width = 1, mini_abun = 0, threshold = 0.02, sample_name, sample_group, mini_tpm = 1000, threshold_tpm = 0.5, both_core_col = 'goldenrod4', common_core_col = 'deeppink4', func_core_col = '#0073C2FF', non_core_col = 'gray', non_hub_col = 'grey', hub_col = 'black')

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