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Barchart of ratio to compare 2 taxonomic ranks

Source: R/compare_taxo_plot.R
tc_bar.Rd

lifecycle-experimental

Useful to compare taxonomy from two different source/db/algo side-by-side

Usage

tc_bar(
  physeq,
  rank_1,
  rank_2,
  color_rank,
  point_size = 0.3,
  point_alpha = 0.3,
  merge_sample_by = NULL,
  log10trans = TRUE
)

Arguments

physeq

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

rank_1

(character or integer) Define the first taxonomic rank as the number or the name of the column in tax_table slot.

rank_2

(character or integer) Define the second taxonomic rank as the number or the name of the column in tax_table slot.

color_rank

(character or integer) Define the taxonomic rank for color as the number or the name of the column in tax_table slot.

point_size

(numeric, default 0.3) Size of points.

point_alpha

(numeric, default 0.3) Transparency of points.

merge_sample_by

(character, default NULL) A vector to determine which samples to merge using MiscMetabar::merge_samples2() function. Need to be in physeq@sam_data.

log10trans

(logical, default TRUE) If TRUE, the abundance is log10 transformed.

Value

A ggplot2 object

Author

Adrien Taudière

Examples


tc_bar(subset_taxa_pq(Glom_otu, taxa_sums(Glom_otu) > 5000), rank_1 = 5, rank_2 = 13, color_rank = 3)
#> Cleaning suppress 0 taxa (  ) and 1 sample(s) ( samp_Blanc-PCR-racines ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1147
#> Number of filtered-out ASV 955
#> Number of kept ASV 192
#> Number of kept samples 443
#> Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
#> ℹ Please use the `fun` argument instead.
#> ℹ The deprecated feature was likely used in the comparpq package.
#>   Please report the issue at
#>   <https://github.com/adrientaudiere/comparpq/issues>.

if (FALSE) { # \dontrun{
tc_bar(Glom_otu, rank_1 = 5, rank_2 = 13, color_rank = 3)
tc_bar(as_binary_otu_table(Glom_otu), rank_1 = 5, rank_2 = 13, color_rank = 3, log10trans = FALSE)
tc_bar(Glom_otu,
  rank_1 = "Genus",
  rank_2 = "Genus__eukaryome_Glomero",
  color_rank = "Family"
)
} # }