Boxplot of selected barcodes

Plots boxplot of counts for selected barcodes from DGEList object.

Usage

plotBarcodeBoxplot(
  dgeObject,
  barcodes = NULL,
  group = NULL,
  conditions = NULL,
  trans = NULL,
  point = FALSE,
  violin = FALSE,
  returnData = FALSE,
  normalizeMethod = "CPM"
)

Arguments

dgeObject

DGEList object with normalized barcode counts.

barcodes

Barcodes to be plotted (vector of strings).

group

Optional, column name in sample metadata to facet data on (string).

conditions

Optional, specific levels of group to be plotted (vector of strings).

trans

Optional, transformation of y-axis, e.g. `log10` (string).

point

Whether to include points (boolean). Default = `FALSE`.

violin

Whether to include violin plots in addition to box plots (boolean). Default = `FALSE`.

returnData

Whether to return data instead of plot (boolean). Default = `FALSE`.

normalizeMethod

Method for normalizing counts (string). One of `CPM`, `TMM`, `TMMwsp`, `upperquartile`, `RLE` or `NULL` for no normalization. See `edgeR::calcNormFactors()`. Default = `CPM`.

Value

Returns a boxplot

Examples

data(test.dge)
plotBarcodeBoxplot(test.dge, barcodes = "BC_190202", group = "Treatment",
conditions = c("Vehicle", "Low_dose", "High_dose"))