plateHeatmap: Plot a plate heatmap

In nbenn/singleCellFeatures: Analyze single cell features stored in an openBIS instance

Description

Given plate data, plot a heatmap of the specified feature using a function to aggregate data within wells and an optional function to transform the resulting vector of length 384.

Usage

plateHeatmap(plate.dat, feature, fun.aggregate = "mean",
  fun.transform = "identity", show.control = TRUE, colors = brewer.pal(9,
  "Reds")[3:9])

Arguments

plate.dat	Data used to generate heatmap. Expecting a PlateData object.
feature	Name of the feature to extract and aggreagte within wells for heatmap plot. Expecting a string.
fun.aggregate	The function used to aggregate data within wells. Expecting either a function object or a string.
fun.transform	An optional function used to transform the data before plotting. Expecting either a function object or a string.
show.control	Logical, whether to mark the control wells.
colors	A vector of colors that is interpolated for the gradient scale.

Value

A ggplot2 plot object ready for printing.

Examples

plate <- PlateLocation("J101-2C")
data  <- PlateData(plate)
plateHeatmap(data, "VoronoiCells.Location_Center_Y", median, sqrt)

nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.