R/utils.R

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

################################################################################
# internal methods loaded from other packages

.check_assay_present <- mia:::.check_assay_present
.require_package <- mia:::.require_package
.check_taxonomic_rank <- mia:::.check_taxonomic_rank
.check_for_taxonomic_data_order <- mia:::.check_for_taxonomic_data_order
.calc_rel_abund <- mia:::.calc_rel_abund

.is_a_bool <- mia:::.is_a_bool
.is_non_empty_character <- mia:::.is_non_empty_character
.is_non_empty_string <- mia:::.is_non_empty_string
.is_a_string <- mia:::.is_a_string
.are_whole_numbers <- mia:::.are_whole_numbers
.is_numeric_string <- mia:::.is_numeric_string
.is_function <- mia:::.is_function
.get_name_in_parent <- mia:::.get_name_in_parent


.norm_label <- function(label, x){
    if(!is.null(label)){
        if(is.numeric(label)){
            n_v <- seq_len(nrow(x))
            if(!all(label %in% n_v)){
                stop("If 'label' is numeric, all values must be between 1 ",
                     "and nrow(x). If rank is not NULL, the dimension might ",
                     "change.",
                     call. = FALSE)
            }
            label <- n_v %in% label
        } else if(is.character(label)){
            if(!all(label %in% rownames(x))){
                stop("If 'label' is character, all values must be in ",
                     "rownames(x). If rank is not NULL, the rownames might ",
                     "change.",
                     call. = FALSE)
            }
            label <- rownames(x) %in% label
        } else if(is.logical(label)){
            if(length(label) != nrow(x)){
                stop("If 'label' is logical, length(label) == nrow(x) mut be ",
                     "TRUE. If rank is not NULL, the rownames might ",
                     "change.",
                     call. = FALSE)
            }
        } else {
            stop("'label' must be a vector.", call. = FALSE)
        }
    }
    label
}