tree_func_plot: tree_func_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

tree_func_plot

Description

Plots phylogenetic tree with a heatmap denoting the average occurrence frequency and average tpm of the functions of each taxa.

Usage

tree_func_plot(
  functional_profile,
  sample,
  tree,
  mini_tpm,
  threshold,
  offset,
  width,
  core_col,
  noncore_col,
  low_col,
  high_col,
  hlab,
  ttip,
  tlab,
  hangle,
  hoffset
)

Arguments

functional_profile	a community count data matrix with samples in rows and OTUs/taxa in column,
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,
mini_tpm	a value indicating whether the function is present,
threshold	a value indicating the final percent increase in beta-diversity,
offset	the offset between each subfigure,
width	the width of each heatmap cell,
core_col	the color of core tips,
noncore_col	the color of non-core tips,
low_col	the lowest color of the heatmap,
high_col	the highest color of the heatmap,
hlab	the font size of the heatmap label,
ttip	the node size of the tree,
tlab	the font size of the tree tip label,

Details

Plots phylogenetic tree with a heatmap denoting the average occurrence frequency and average tpm of the functions of each taxa.

Value

A phylogenetic tree with a heatmap denoting the average occurrence frequency and average tpm of the functions of each taxa with color denoting and core or non-core functional otu.

Examples

 tree_func_plot(functional_profile, sample, tree, mini_tpm=1000, threshold=0.5, offset = 0.1, width = 0.5, core_col = 'deeppink4', noncore_col = 'darkseagreen3', low_col = 'white', high_col = 'lightcoral', hlab = 2, ttip = 2, tlab = 2, hangle = 270, hoffset = -1)

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