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(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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29
R/top_n_microorganisms.R
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@ -28,7 +28,7 @@
# ==================================================================== #
#' Filter Top *n* Microorganisms
#'
#'
#' This function filters a data set to include only the top *n* microorganisms based on a specified property, such as taxonomic family or genus. For example, it can filter a data set to the top 3 species, or to any species in the top 5 genera, or to the top 3 species in each of the top 5 genera.
#' @param x a data frame containing microbial data
#' @param n an integer specifying the maximum number of unique values of the `property` to include in the output
@ -42,15 +42,18 @@
#' @examples
#' # filter to the top 3 species:
#' top_n_microorganisms(example_isolates,
#' n = 3)
#'
#' n = 3
#' )
#'
#' # filter to any species in the top 5 genera:
#' top_n_microorganisms(example_isolates,
#' n = 5, property = "genus")
#'
#' n = 5, property = "genus"
#' )
#'
#' # filter to the top 3 species in each of the top 5 genera:
#' top_n_microorganisms(example_isolates,
#' n = 5, property = "genus", n_for_each = 3)
#' n = 5, property = "genus", n_for_each = 3
#' )
top_n_microorganisms <- function(x, n, property = "fullname", n_for_each = NULL, col_mo = NULL, ...) {
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(n, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE, is_positive = TRUE)
@ -61,25 +64,25 @@ top_n_microorganisms <- function(x, n, property = "fullname", n_for_each = NULL,
col_mo <- search_type_in_df(x = x, type = "mo", info = TRUE)
stop_if(is.null(col_mo), "`col_mo` must be set")
}
x.bak <- x
x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE], keep_synonyms = TRUE)
if (is.null(property)) {
x$prop_val <- x[[col_mo]]
} else {
x$prop_val <- mo_property(x[[col_mo]], property = property, ...)
}
counts <- sort(table(x$prop_val), decreasing = TRUE)
n <- as.integer(n)
if (length(counts) < n) {
n <- length(counts)
}
count_values <- names(counts)[seq_len(n)]
filtered_rows <- which(x$prop_val %in% count_values)
filtered_rows <- which(x$prop_val %in% count_values)
if (!is.null(n_for_each)) {
n_for_each <- as.integer(n_for_each)
filtered_x <- x[filtered_rows, , drop = FALSE]
@ -92,6 +95,6 @@ top_n_microorganisms <- function(x, n, property = "fullname", n_for_each = NULL,
})
)
}
x.bak[filtered_rows, , drop = FALSE]
}