Rainplot of the nb taxa assigned (not NA)

Useful to compare taxonomy from two different source/db/algo

Usage

rainplot_taxo_na(
  physeq,
  ranks = NULL,
  min_nb_seq = 0,
  merge_sample_by = NULL,
  sample_colored = FALSE,
  sample_linked = FALSE,
  ...
)

Arguments

physeq

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

ranks

(character or integer vector, default NULL) The ranks to include in the rainplot. If left to NULL, all ranks are used. Each rank can be defined either by integer for the index or by its full names (exactly matching the colnames of the tax_table slot).

min_nb_seq

(integer, default 0) Minimum number of sequences to filter out taxa with low abundance.

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.

sample_colored

(logical, default FALSE) If TRUE, points are colored by samples.

sample_linked

(logical, default FALSE) If TRUE, points are linked by samples.

...

Additional arguments passed to ggrain::geom_rain().

Value

A ggplot2 object

Author

Adrien Taudière

Examples

rainplot_taxo_na(subset_taxa_pq(Glom_otu, taxa_sums(Glom_otu) > 5000),
  ranks = c("Family", "Family__eukaryome_Glomero")
)
#> 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
#> Registered S3 methods overwritten by 'ggpp':
#>   method                  from   
#>   heightDetails.titleGrob ggplot2
#>   widthDetails.titleGrob  ggplot2

if (FALSE) { # \dontrun{
rainplot_taxo_na(Glom_otu)

Glom_otu@sam_data$tmt_type <- paste0(Glom_otu@sam_data$Tmt, "_", Glom_otu@sam_data$Type)
rainplot_taxo_na(
  Glom_otu,
  merge_sample_by = "tmt_type",
  sample_colored = TRUE,
  sample_linked = TRUE
)
rainplot_taxo_na(Glom_otu, ranks = c(4, 12), rain.side = "f1x1")
rainplot_taxo_na(
  Glom_otu,
  ranks = c(6, 14),
  rain.side = "f1x1",
  sample_linked = TRUE
) +
  theme(legend.position = "none")
} # }