plotly_quartiles: Make a line-based alternative to boxplots

In pinin4fjords/shinyngs: Shiny apps for NGS data

Make a line-based alternative to boxplots

Description

Box-plots become unmanagable with large numbers of samples. This function plots lines at the median, quartiles, and whiskers, plotting points for outliers beyond that

Usage

plotly_quartiles(
  matrix,
  labels = rownames(matrix),
  expressiontype = "expression",
  whisker_distance = 1.5,
  should_transform = NULL
)

Arguments

matrix	Numeric matrix
labels	String vector of labels to be used for each matrix row
expressiontype	Y axis label
whisker_distance	IQR multiplier for whiskers, and beyond which to show outliers (see coef in geom_boxplot)
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.

Examples

data(airway, package = "airway")
plotly_quartiles(assays(airway)[[1]], as(airway, "ExploratorySummarizedExperiment"))

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