Plot gene detection saturation

We should observe a linear trend in the number of genes detected with the number of mapped reads, which indicates that the sample input was not overloaded.

plotGeneSaturation(object, ...)

# S4 method for bcbioRNASeq
plotGeneSaturation(object,
  interestingGroups = NULL, minCounts = 1L, perMillion = TRUE,
  trendline = FALSE, label = getOption(x = "acid.label", default =
  FALSE), color = getOption(x = "acid.color.discrete", default =
  acidplots::scale_color_synesthesia_d()), labels = list(title =
  "Gene saturation", subtitle = NULL, x = "mapped reads", y =
  "gene count"))

Arguments

object	Object.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
minCounts	integer(1). Minimum number of counts per feature (i.e. gene).
perMillion	logical(1). Display as counts per million.
trendline	logical(1). Include trendline on plot.
label	logical(1). Superimpose sample text labels on the plot.
color	ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual(). To set the discrete color palette globally, use: options(acid.color.discrete = ggplot2::scale_color_viridis_d())
labels	list. ggplot2 labels. See ggplot2::labs() for details.
...	Additional arguments.

Value

ggplot.

Note

Updated 2019-09-16.

Examples

data(bcb)
plotGeneSaturation(bcb, label = FALSE)
plotGeneSaturation(bcb, label = TRUE)