parse_tax_and_plot: Metacoder plot

In surh/wheelP: Designing synthetic bacterial communities for predictable plant phenotypes

Description

Creates a metacoder heat tree plot. Normally it should be called throught the metacoder_plot_go.

Usage

parse_tax_and_plot(file, col, output_file = output_file,
  n.supertaxa = n.supertaxa, num.changed = num.changed, min_fdr = min_fdr)

Arguments

file	A filename of the gene ontologies to include. The function metacoder_plot_go generates this file and passes it to this function automatically.
col	Which column to use for coloring.
output_file	Name of the file to save the plot.
n.supertaxa	How much to extend the network fri the root node.
num.changed	Minimun number of genes with a given annotation to include that annotation
min_fdr	False discovery rate threshold

Details

Requires you to load metacoder package, otherwise names do not print.

Value

The data from the heat_tree function.

Author(s)

Code from metacoder paper with small adaptations by Sur Herrera Paredes

References

Foster ZSL, Sharpton TJ, Gr<c3><bc>nwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 13(2): e1005404. https://doi.org/10.1371/journal.pcbi.1005404

See Also

metacoder_plot_go heat_tree

surh/wheelP documentation built on May 7, 2019, 10:11 a.m.