plotAssayRaw-methods: Plot the raw assayData

In steveped/incucyteR: Process Incucyte Growth Curve Data

Description

Plot the raw assayData from an IncucyteExperiment object

Usage

plotAssayRaw(x, assay, ..., trans = "log10", facet = facet_grid(row ~ col))

## S4 method for signature 'ANY'
plotAssayRaw(x, assay, ..., trans = "log10", facet = facet_grid(row ~ col))

## S4 method for signature 'IncucyteExperiment'
plotAssayRaw(x, assay, ..., trans = "log10", facet = facet_grid(row ~ col))

Arguments

x	An IncucyteExperiment object
assay	The assay to be visualised
...	Passed to aes_string() in the initial call to ggplot. Any aesthetics can be specified here, with values passed to the aesthetics as a character, and that match a column name from colData.
trans	The transformation for the y-axis
facet	Faceting to add to the plot

Details

Visualise all data from the requested assay. By default a line plot will be produced for every image within each well. The plot will also be broken into facets using the row and column information.

Lines can be coloured by any additional column contained in the colData slot of the IncucyteExperiment object by setting the argument colour = colName, which will be passed to aes_string() within the initial call to ggplot. Any additional columns must be quoted.

Additional information can also be added to the facet headers by adding the column you wish. For example, if each column contains a unique CellType, you could specify facet = facet_grid(row~col+CellType). Note that any additional column must also be contained in the colData slot.

The returned object is a ggplot object and can be further modified using scales, themes and additional geoms.

Value

A ggplot object

steveped/incucyteR documentation built on Sept. 7, 2020, 12:22 p.m.