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Make a boxplot with coloring by experimental variable

Source: R/boxplot.R
static_boxplot.Rd

A simple function using ggplot2 to make a sample boxplot

Usage

static_boxplot(
  plotmatrices,
  experiment,
  colorby = NULL,
  palette = NULL,
  expressiontype = "expression",
  whisker_distance = 1.5,
  base_size = 11,
  palette_name = COLORBLIND_PALETTE_NAME,
  annotate_samples = FALSE,
  should_transform = NULL
)

Arguments

plotmatrices

Expression/ other data matrix, or named list thereof

experiment

Annotation for the columns of plotmatrix

colorby

Column name in experiment specifying how boxes should be colored

palette

Palette of colors, one for each unique value derived from colorby.

expressiontype

Expression type for use in y axis label

whisker_distance

Passed to geom_boxplot as coef, controlling the length of the whiskers. See documentation of that function for more info (default: 1.5).

base_size

Passed to ggplot's theme()

palette_name

Valid R color palette name

annotate_samples

Add a suffix to sample labels reflecting their group?

should_transform

A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.

Value

output A ggplot output

Examples

require(airway)
data(airway, package = "airway")
static_boxplot(assays(airway)[[1]], data.frame(colData(airway)), colorby = "dex")