metacoder_plot_go: Plot GO from edgeR

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

Description

Creates a metacoder network plot from gene ontologies. Figures from this function where not included in final manuscript.

Usage

metacoder_plot_go(dat, output_folder = "./", output_format = "svg",
  min_fdr = 0.01, type = GO.db::GOBPPARENTS, prefix = "go",
  n.supertaxa = 9, num.changed = 3)

Arguments

dat	A data frame containing the results of differential expression analysis on edgeR. The data frame is the result of performing hypothesis testing, for example with the likelihood ratio test (i.e. function glmLRT).
output_folder	Charachter string indicating the directory to store the plots.
output_format	Format of the image to save. It must be allowed by the heat_tree function.
min_fdr	False discovery rate threshold to filter genes. Only genes with a smaller fdr and their annotations will be included.
type	This must be an object that specifies the parents of each annotation terms. Default is object GOBPPARENTS fromthe GO.db bioconductor package, but any other simular object can be used.
prefix	Character string. Prefix for file names.
n.supertaxa	Number of levels to extend the tree.
num.changed	Minimum number of genes in an annotation category fir that annotation to be included.

Details

The script takes a list of differentially expressed genes and their GO annotations and creates a tree representing the gene ontologies present and color codes it by the overal log(fold-change) im expression/

Value

The data used by link{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

parse_tax_and_plot heat_tree

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