R/deprecated.R

Defines functions writeCounts topTables prepareRNASeqTemplate plotRRNAMappingRate plotQC plotPCACovariates plotPCA plotMeanSD plotMeanAverage plotMA plotGenesDetected plotGeneSaturation plotDEGHeatmap plotCountsPerGene camel

Documented in camel plotCountsPerGene plotDEGHeatmap plotGeneSaturation plotGenesDetected plotMA plotMeanAverage plotMeanSD plotPCA plotPCACovariates plotQC plotRRNAMappingRate prepareRNASeqTemplate topTables writeCounts

#' @name deprecated
#' @inherit AcidRoxygen::deprecated description examples return seealso title
#' @inheritParams AcidRoxygen::params
#' @keywords internal
NULL



#' @export
#' @rdname deprecated
camel <- function(...) {
    .Deprecated("syntactic::camelCase")
    assert(requireNamespaces("syntactic"))
    syntactic::camelCase(...)
}



#' @export
#' @rdname deprecated
plotCountsPerGene <- function(object, ...) {
    .Deprecated("plotCountsPerFeature")
    assert(.isGeneLevel(object))
    plotCountsPerFeature(object, ...)
}



#' @export
#' @rdname deprecated
plotDEGHeatmap <- function(...) {
    .Deprecated("DESeqAnalysis::plotDegHeatmap")
    assert(requireNamespaces("DESeqAnalysis"))
    DESeqAnalysis::plotDegHeatmap(...)
}



`plotDegHeatmap,deprecated` <- # nolint
    function(object, results, counts, ...) {
        assert(
            is(results, "DESeqResults"),
            is(counts, "DESeqTransform")
        )
        plotDegHeatmap(
            object = results,
            DESeqTransform = counts,
            ...
        )
    }

#' @export
#' @rdname deprecated
#' @param `results` `DESeqResults.`
#' @param `counts` `DESeqTransform`.
setMethod(
    f = "plotDegHeatmap",
    signature = signature(object = "missing"),
    definition = `plotDegHeatmap,deprecated`
)



#' @export
#' @rdname deprecated
plotGeneSaturation <- function(object, ...) {
    .Deprecated("plotFeatureSaturation")
    assert(.isGeneLevel(object))
    plotFeatureSaturation(object, ...)
}



#' @export
#' @rdname deprecated
plotGenesDetected <- function(object, ...) {
    .Deprecated("plotFeaturesDetected")
    assert(.isGeneLevel(object))
    plotFeaturesDetected(object, ...)
}



#' @export
#' @rdname deprecated
plotMA <- function(...) {
    .Deprecated("DESeqAnalysis::plotMa")
    assert(requireNamespaces("DESeqAnalysis"))
    DESeqAnalysis::plotMa(...)
}



#' @export
#' @rdname deprecated
plotMeanAverage <- function(...) {
    .Deprecated("DESeqAnalysis::plotMa")
    assert(requireNamespaces("DESeqAnalysis"))
    DESeqAnalysis::plotMa(...)
}



#' @export
#' @rdname deprecated
plotMeanSD <- function(...) {
    .Deprecated("plotMeanSd")
    plotMeanSd(...)
}



#' @export
#' @rdname deprecated
plotPCA <- function(...) {
    .Deprecated("plotPca")
    plotPca(...)
}



#' @export
#' @rdname deprecated
plotPCACovariates <- function(...) {
    .Deprecated("plotPcaCovariates")
    plotPcaCovariates(...)
}



#' @export
#' @rdname deprecated
plotQC <- function(...) {
    .Deprecated("plotQc")
    plotQc(...)
}



#' @export
#' @rdname deprecated
plotRRNAMappingRate <- function(...) {
    .Deprecated("plotRrnaMappingRate")
    plotRrnaMappingRate(...)
}



#' @export
#' @rdname deprecated
prepareRNASeqTemplate <- function(...) {
    .Deprecated("AcidMarkdown::prepareTemplate")
    assert(requireNamespaces("AcidMarkdown"))
    AcidMarkdown::prepareTemplate(...)
}



#' @export
#' @rdname deprecated
topTables <- function(...) {
    .Deprecated("DESeqAnalysis::markdownTables")
    assert(requireNamespaces("DESeqAnalysis"))
    DESeqAnalysis::markdownTables(...)
}



#' @export
#' @rdname deprecated
writeCounts <-
    function(...,
             dir = getOption(x = "acid.export.dir", default = getwd())) {
        .Deprecated("export")
        objects <- list(...)
        names(objects) <- dots(..., character = TRUE)
        out <- Map(
            object = objects,
            con = file.path(dir, paste0(names(objects), ".csv")),
            f = export
        )
        invisible(out)
    }
hbc/bcbioRNASeq documentation built on Jan. 16, 2024, 1:43 a.m.