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Make an interactive boxplot with coloring by experimental variable

Source: R/boxplot.R
interactive_boxplot.Rd

Draws a plotly box plot of the value distribution in each sample. Box statistics (quartiles, whiskers, outliers) are computed server-side and supplied to plotly as precomputed values, so the browser payload scales with the number of samples rather than the size of the matrix. This makes it usable on full expression matrices where sending every point would not be.

Usage

interactive_boxplot(
  plotmatrices,
  experiment,
  colorby = NULL,
  palette = NULL,
  expressiontype = "expression",
  palette_name = COLORBLIND_PALETTE_NAME,
  whisker_distance = 1.5,
  annotate_samples = FALSE,
  should_transform = NULL,
  max_outliers = 500,
  hidden_groups = character(0),
  source = 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

palette_name

Valid R color palette name

whisker_distance

IQR multiplier for the whiskers, and the boundary beyond which points are drawn as outliers (see coef in geom_boxplot, default: 1.5)

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.

max_outliers

Maximum number of outlier points to draw per facet. When a sample set produces more, the most extreme (furthest from the median) are kept so the overlay stays bounded (default: 500).

hidden_groups

Values of colorby to exclude: their samples are dropped so the plot is redrawn on the remainder, while they stay in the legend (as legendonly) so they can be toggled back on.

source

Optional plotly source id used to route legend-click (plotly_restyle) events back to a Shiny session.

Value

output A plotly output

Examples

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