Sankey diagram to compare two taxonomic ranks

Creates a Sankey (alluvial) diagram to visualize the correspondence between two taxonomic ranks. Useful for comparing taxonomy assignments from different databases or algorithms.

Usage

tc_sankey(physeq, rank_1, rank_2, fill_by = "rank_1")

Arguments

physeq: (required) A phyloseq-class object obtained using the phyloseq package.
rank_1: (character or integer, required) Define the first taxonomic rank as the number or the name of the column in tax_table slot.
rank_2: (character or integer, required) Define the second taxonomic rank as the number or the name of the column in tax_table slot.
fill_by: (character, default "rank_1") Which rank to use for fill color. Either "rank_1" or "rank_2".

Value

A ggplot2 object that can be further customized.

Author

Adrien Taudière

Examples

tc_sankey(
  Glom_otu,
  "Class__eukaryome_Glomero",
  "Class"
)
#> Warning: Some strata appear at multiple axes.
#> Warning: Some strata appear at multiple axes.


# Fill by rank_2 instead
tc_sankey(
  Glom_otu,
  "Class__eukaryome_Glomero",
  "Class",
  fill_by = "rank_2"
)
#> Warning: Some strata appear at multiple axes.
#> Warning: Some strata appear at multiple axes.


if (FALSE) { # \dontrun{
# Add labels to the strata
tc_sankey(Glom_otu, "Class__eukaryome_Glomero", "Class") +
  geom_label(
    stat = "stratum",
    aes(label = after_stat(stratum)),
    na.rm = TRUE
  ) +
  theme(legend.position = "none")
} # }