phnetworks: phnetworks

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

phnetworks

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

phnetworks(
  otu,
  taxa,
  sample,
  tree,
  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
)

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,
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,

Details

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.

Value

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

Examples

 phnetworks(otu, taxa, sample, tree, 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)

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