plot_edgeR_pq: Plot edgeR results for a phyloseq or a edgeR object.

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot edgeR results for a phyloseq or a edgeR object.

Description

Graphical representation of edgeR result.

Usage

plot_edgeR_pq(
  physeq,
  contrast = NULL,
  pval = 0.05,
  taxolev = "Genus",
  color_tax = "Phylum",
  verbose = TRUE,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
contrast	(required):This argument specifies what comparison to extract from the object to build a results table. See results man page for more details.
pval	(default: 0.05): the significance cutoff used for optimizing the independent filtering. If the adjusted p-value cutoff (FDR) will be a value other than 0.05, pval should be set to that value.
taxolev	taxonomic level of interest
color_tax	taxonomic level used for color assignation
verbose	(logical): whether the function print some information during the computation
...	Additional arguments passed on to exactTest or ggplot

Value

A ggplot2 plot representing edgeR results

Author(s)

Adrien Taudière

See Also

exactTest

plot_deseq2_pq

Examples

data("GlobalPatterns", package = "phyloseq")
GP_archae <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")

if (requireNamespace("edgeR")) {
  plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
    color_tax = "Kingdom"
  )

  plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
    taxolev = "Class", color_tax = "Kingdom"
  )
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.