assayBoxPlot {karyotapR}

Generate a box plot from assay data

Description

Draws box plot of data from indicated TapestriExperiment assay slot. This is especially useful for visualizing altExp count data, such as counts from probes on chrY or barcode probe counts.

Usage

assayBoxPlot(
  TapestriExperiment,
  alt.exp = NULL,
  assay = NULL,
  log.y = TRUE,
  split.features = FALSE,
  split.x.by = NULL,
  split.y.by = NULL
)

Arguments

TapestriExperiment

TapestriExperiment object

alt.exp

Character, altExp to plot. NULL (default) uses the top-level experiment in TapestriExperiment.

assay

Character, assay to plot. NULL (default) selects first assay listed TapestriExperiment.

log.y

Logical, if TRUE, scales data using log1p(). Default TRUE.

split.features

Logical, if TRUE, splits plot by rowData features if slot has more than one row feature/probe. Default FALSE.

split.x.by

Character, colData column to use for X-axis categories. Default NULL.

split.y.by

Character, colData column to use for Y-axis splitting/faceting. Default NULL.

Value

ggplot object, box plot

See Also

ggplot2::geom_boxplot()

Examples

tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
assayBoxPlot(tap.object, alt.exp = "chrYCounts", split.features = TRUE, split.x.by = "test.cluster")