phfunc: phfunc

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

phfunc

Description

Constructs a plot combining the phylogenetic tree, the heatmaps showing average occurrence frequency and average relative abundance of each taxa.

Usage

phfunc(
  otu,
  taxa,
  sample,
  tree,
  functional_profile,
  pre_threshold,
  hcol = "red",
  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
)

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,
pre_threshold	occurrence frequency,
hcol	the color of heatmap,
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

Details

Constructs a plot combining the phylogenetic tree, the heatmaps showing average occurrence frequency and average relative abundance of each taxa.

Value

Combined plot showing the phylogenetic tree and the heatmaps.

Examples

 phfunc(otu, taxa, sample, tree, functional_profile, pre_threshold, hcol = 'red', 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')

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