parse_tax_and_plot: Metacoder plot

Description Usage Arguments Details Value Author(s) References See Also

View source: R/parse_tax_and_plot.r

Description

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

Usage

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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, Grünwald 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 Feb. 21, 2018, 7:40 p.m.