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Heat tree from metacoder package using tax_table slot

Source: R/plot_functions.R
heat_tree_pq.Rd

lifecycle-maturing

Note that the number of ASV is store under the name n_obs and the number of sequences under the name nb_sequences

Usage

heat_tree_pq(physeq, taxonomic_level = NULL, ...)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

taxonomic_level

(default: NULL): a vector of selected taxonomic level using their column numbers (e.g. taxonomic_level = 1:7)

...

Arguments passed on to heat_tree

Value

A plot

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("metacoder")) {
  library("metacoder")
  data("GlobalPatterns", package = "phyloseq")

  GPsubset <- subset_taxa(
    GlobalPatterns,
    GlobalPatterns@tax_table[, 1] == "Bacteria"
  )

  GPsubset <- subset_taxa(
    GPsubset,
    rowSums(GPsubset@otu_table) > 5000
  )

  GPsubset <- subset_taxa(
    GPsubset,
    rowSums(is.na(GPsubset@tax_table)) == 0
  )

  heat_tree_pq(GPsubset,
    node_size = n_obs,
    node_color = n_obs,
    node_label = taxon_names,
    tree_label = taxon_names,
    node_size_trans = "log10 area"
  )

  heat_tree_pq(GPsubset,
    node_size = nb_sequences,
    node_color = n_obs,
    node_label = taxon_names,
    tree_label = taxon_names,
    node_size_trans = "log10 area"
  )
}
#> Loading required namespace: metacoder
#> This is metacoder version 0.3.7 (stable)
#> 
#> Attaching package: ‘metacoder’
#> The following object is masked from ‘package:ggplot2’:
#> 
#>     map_data
#> The following object is masked from ‘package:phyloseq’:
#> 
#>     filter_taxa
#> 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’
#> Error in eval(e, x, parent.frame()): object 'GPsubset' not found
# }