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The S4 generic `ps_tibble()` was developed in place of `as_tibble()` methods to avoid issue #61. However, this issue was due to speedyseq defining an S4 generic `as_tibble()` in addition to the S3 methods for `tibble::as_tibble()`. Defining S3 methods alone seems sufficient for the desired behavior without an addition S4 method. Other changes: Import tibble in joins example; rebuild site.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| #' @importFrom tibble as_tibble | ||
| tibble::as_tibble | ||
|
|
||
| #' Coerce phyloseq objects to tibble data frames | ||
| #' | ||
| #' These functions extend the `as_tibble()` function defined by the tibble | ||
| #' package to work on phyloseq objects or phyloseq-component objects. | ||
| #' | ||
| #' Tibbles (tbl_df objects) do not support rownames; the taxa and sample names | ||
| #' in the returned tibbles will always be stored in the first or second | ||
| #' columns. The names ".otu", ".sample", ".abundance", and ".sequence" are | ||
| #' special column names reserved for the otu/taxa names, sample names, | ||
| #' abundances, and reference sequences. | ||
| #' | ||
| #' @param x A phyloseq object or component. | ||
| #' @param pivot Whether to pivot the otu table to long format. | ||
| #' @param tax Whether to include taxonomy data. | ||
| #' @param ref Whether to include reference sequences. | ||
| #' @param .name_repair Function to repair names in the case of conflicts. | ||
| #' | ||
| #' @return A tibble (tbl_df) | ||
| #' | ||
| #' @name as_tibble-phyloseq | ||
| #' | ||
| #' @examples | ||
| #' library(tibble) # for as_tibble() and glimpse() | ||
| #' | ||
| #' data(GlobalPatterns) | ||
| #' | ||
| #' # Subset to 1/100 of the original taxa to speed operations | ||
| #' ps <- GlobalPatterns %>% | ||
| #' filter_tax_table(dplyr::row_number() %% 100 == 1) | ||
| #' | ||
| #' # On phyloseq objects, as_tibble is similar to psmelt() | ||
| #' psmelt(ps) %>% glimpse | ||
| #' as_tibble(ps) %>% glimpse | ||
| #' | ||
| #' # By default, the otu_table method provides a tibble in long-format like | ||
| #' # psmelt and the phyloseq method | ||
| #' otu_table(ps) %>% as_tibble %>% glimpse | ||
| #' | ||
| #' # Sample data and taxonomy tables produced by as_tibble can be converted | ||
| #' # back into their respective phyloseq objects using speedyseq's tbl_df | ||
| #' # constructors | ||
| #' sample_data(ps) <- sample_data(ps) %>% | ||
| #' as_tibble %>% | ||
| #' dplyr::mutate(sample_sum = sample_sums(ps)) %>% | ||
| #' sample_data | ||
| #' sample_data(ps) %>% glimpse | ||
| NULL | ||
|
|
||
| #' @export | ||
| #' @rdname as_tibble-phyloseq | ||
| as_tibble.otu_table <- function(x, | ||
| pivot = TRUE, | ||
| .name_repair = base::make.unique) { | ||
| mat <- x %>% as("matrix") | ||
| if (pivot) { | ||
| if (!taxa_are_rows(x)) | ||
| mat <- t(mat) | ||
| tb <- mat %>% | ||
| tibble::as_tibble(rownames = ".otu") %>% | ||
| tidyr::pivot_longer( | ||
| cols = sample_names(x), | ||
| names_to = ".sample", | ||
| values_to = ".abundance" | ||
| ) | ||
| } else { | ||
| rn <- ifelse(taxa_are_rows(x), ".otu", ".sample") | ||
| tb <- mat %>% | ||
| tibble::as_tibble(rownames = rn) %>% | ||
| rlang::set_names(., | ||
| vctrs::vec_as_names(names(.), repair = .name_repair) | ||
| ) | ||
| } | ||
| tb | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname as_tibble-phyloseq | ||
| as_tibble.sample_data <- function(x, .name_repair = base::make.unique) { | ||
| x %>% | ||
| as("data.frame") %>% | ||
| tibble::as_tibble(rownames = ".sample") %>% | ||
| rlang::set_names(., | ||
| vctrs::vec_as_names(names(.), repair = .name_repair) | ||
| ) | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname as_tibble-phyloseq | ||
| as_tibble.taxonomyTable <- function(x, .name_repair = base::make.unique) { | ||
| x %>% | ||
| as("matrix") %>% | ||
| tibble::as_tibble(rownames = ".otu") %>% | ||
| rlang::set_names(., | ||
| vctrs::vec_as_names(names(.), repair = .name_repair) | ||
| ) | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname as_tibble-phyloseq | ||
| as_tibble.XStringSet <- function(x) { | ||
| x %>% | ||
| as.character %>% | ||
| tibble::enframe(".otu", ".sequence") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname as_tibble-phyloseq | ||
| as_tibble.phyloseq <- function(x, | ||
| tax = TRUE, | ||
| ref = FALSE, | ||
| .name_repair = base::make.unique) { | ||
| tb <- otu_table(x) %>% as_tibble(pivot = TRUE) | ||
| # Add sample data if it exists | ||
| sam <- access(x, "sam_data") | ||
| if (!is.null(sam)) { | ||
| tb <- tb %>% | ||
| dplyr::left_join( | ||
| sam %>% as_tibble(.name_repair = .name_repair), | ||
| by = ".sample", | ||
| suffix = c("", ".sam") | ||
| ) | ||
| } | ||
| # Add tax_table if it exists and tax = TRUE | ||
| tt <- access(x, "tax_table") | ||
| if (tax & !is.null(tt)) { | ||
| tb <- tb %>% | ||
| dplyr::left_join( | ||
| tt %>% as_tibble(.name_repair = .name_repair), | ||
| by = ".otu", | ||
| suffix = c("", ".tax") | ||
| ) | ||
| } | ||
| # Add refseq if it exists and ref = TRUE | ||
| rs <- access(x, "refseq") | ||
| if (ref & !is.null(rs)) { | ||
| tb <- tb %>% | ||
| dplyr::left_join( | ||
| rs %>% as_tibble, | ||
| by = ".otu", | ||
| suffix = c("", ".ref") | ||
| ) | ||
| } | ||
| tb | ||
| } |
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