R/deprecation-utils.R

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

#' @noRd
#' @keywords internal
#' @examples
#' .deprecatedDotParam("test_me", "n.folds", "1.21")
#'
.deprecatedDotParam <- function(funName,
                                argumentName,
                                newArgumentName = gsub(
                                    "\\.(\\w)", "\\U\\1",
                                    argumentName,
                                    perl = TRUE
                                ),
                                version = "1.21.0",
                                env = rlang::caller_env(),
                                userEnv = rlang::caller_env(2)) {
    lifecycle::deprecate_warn(
        version,
        paste0(funName, "(", argumentName, " = )"),
        paste0(funName, "(", newArgumentName, " = )"),
        env = env,
        user_env = userEnv
    )
}

#' @rdname balancedCvFolds
#' @usage # deprecated, please use balancedCvFolds()
#' balanced.cv.folds(..., nfolds = 10)
balanced.cv.folds <- function(..., nfolds = 10) { # nolint: object_name_linter.
    lifecycle::deprecate_soft(
        "1.21.0", "balanced.cv.folds()", "balanced_cv_folds()"
    )
    balancedCvFolds(..., nfolds = nfolds)
}

#' @rdname myColors
#' @usage # deprecated, please use myColors()
#' my.colors(ix = NULL)
#' @export
my.colors <- function(ix = NULL) { # nolint: object_name_linter.
    lifecycle::deprecate_soft("1.21.0", "my.colors()", "myColors()")
    myColors(ix)
}

#' @rdname mySymbols
#' @usage # deprecated, please use mySymbols()
#' my.symbols(ix = NULL)
#' @export
my.symbols <- function(ix = NULL) { # nolint: object_name_linter.
    lifecycle::deprecate_soft("1.21.0", "my.symbols()", "mySymbols()")
    mySymbols(ix)
}

#' Retrieve hallmarks of cancer count for genes
#'
#' `r lifecycle::badge("defunct")`
#' The API has been removed and this function is no longer available.
#'
#' @param genes gene names
#' @param metric see below
#' @param hierarchy see below
#' @param generate.plot flag to indicate if return object has a ggplot2 object
#' @param show.message flag to indicate if run_cache method shows messages
#'
#' @return data.frame with choosen metric and hierarchy
#' It also returns a vector with genes that do not have any
#' hallmarks.
#'
#' See http://chat.lionproject.net/api for more details on the
#' metric and hallmarks parameters
#'
#' To standardize the colors in the gradient you can use
#' scale_fill_gradientn(limits=c(0,1), colours=topo.colors(3)) to
#' limit between 0 and 1 for cprob and -1 and 1 for npmi
#'
#' @export
hallmarks <- function(genes,
                      metric = "count",
                      hierarchy = "full",
                      generate.plot = TRUE, # nolint: object_name_linter.
                      show.message = FALSE) { # nolint: object_name_linter.
    lifecycle::deprecate_stop(
        "1.21.0", "hallmarks()",
        details = "API is no longer available"
    )
}