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Plot edgeR results for a phyloseq or a edgeR object.

Source: R/Deseq2_edgeR.R
plot_edgeR_pq.Rd

lifecycle-maturing

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

See also

exactTest

plot_deseq2_pq

Author

Adrien Taudière

Examples

data("GlobalPatterns", package = "phyloseq")
GP_archae <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
# \donttest{
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"
  )
}
#> Conversion to edgeR format
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Perform edgeR binary test
#> Conversion to edgeR format
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Perform edgeR binary test

# }