assayBoxPlot: Generate a box plot from assay data

In karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels

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")

karyotapR documentation built on Sept. 8, 2023, 5:07 p.m.