ggplot_boxplot: Make a boxplot with coloring by experimental variable

In pinin4fjords/shinyngs: Shiny apps for NGS data

Make a boxplot with coloring by experimental variable

Description

A simple function using ggplot2 to make a sample boxplot

Usage

ggplot_boxplot(
  plotmatrices,
  experiment,
  colorby = NULL,
  palette = NULL,
  expressiontype = "expression",
  whisker_distance = 1.5,
  base_size = 11,
  palette_name = "Set1",
  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")
ggplot_boxplot(assays(airway)[[1]], data.frame(colData(airway)), colorby = "dex")

pinin4fjords/shinyngs documentation built on Jan. 18, 2025, 7:09 p.m.