Plot Sexually Dimorphic Gender Markers

Plot Sexually Dimorphic Gender Markers

plotGenderMarkers(object, ...)

# S4 method for bcbioRNASeq
plotGenderMarkers(object,
  color = scale_color_viridis(discrete = TRUE))

# S4 method for DESeqDataSet
plotGenderMarkers(object, organism,
  color = scale_color_viridis(discrete = TRUE))

# S4 method for matrix
plotGenderMarkers(object, organism, ylab = "counts",
  color = scale_color_viridis(discrete = TRUE))

Arguments

object	Object.
...	Additional arguments (for the S4 generic definition).
color	Desired ggplot color scale. Defaults to viridis::scale_color_viridis(). Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().
organism	Optional. Organism name. Should be detected automatically, unless a spike-in FASTA sequence is provided containing a gene identifier that is first alphabetically in the count matrix rownames.
ylab	Y-axis label.

Value

ggplot.

See also

Other Quality Control Plots: plot53Bias, plotCountDensity, plotCountsPerGene, plotExonicMappingRate, plotGeneSaturation, plotGenesDetected, plotGene, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotRRNAMappingRate, plotTotalReads

Examples

# Use F1000 workflow example dataset
# The minimal example inside the package doesn't have dimorphic genes
# NOT RUN {
loadRemoteData(
    file.path(
        "https://github.com",
        "hbc",
        "bcbioRNASeq",
        "raw",
        "f1000v1",
        "data",
        "bcb.rda"
    )
)
plotGenderMarkers(bcb)
# }