#' Plot Mitochondrial Transcript Abundance
#'
#' @name plotMitoRatio
#' @family Quality Control Functions
#' @author Michael Steinbaugh, Rory Kirchner
#'
#' @inheritParams general
#'
#' @return `ggplot`.
#'
#' @examples
#' # SingleCellExperiment ====
#' plotMitoRatio(cellranger_small)
NULL
# Methods ======================================================================
#' @rdname plotMitoRatio
#' @export
setMethod(
"plotMitoRatio",
signature("SingleCellExperiment"),
function(
object,
geom = c("ecdf", "ridgeline", "violin", "histogram", "boxplot"),
interestingGroups,
max = 1L,
fill = NULL,
trans = "sqrt",
title = "mito ratio"
) {
geom <- match.arg(geom)
assert_all_are_in_left_open_range(max, lower = 0L, upper = 1L)
.plotQCMetric(
object = object,
metricCol = "mitoRatio",
geom = geom,
interestingGroups = interestingGroups,
max = max,
trans = trans,
ratio = TRUE,
fill = fill,
title = title
)
}
)
#' @rdname plotMitoRatio
#' @export
setMethod(
"plotMitoRatio",
signature("seurat"),
getMethod("plotMitoRatio", "SingleCellExperiment")
)
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