Sample assay plot defaults

Description

Create default settings for sample assay plot panels in the iSEE interface.

Usage

sampAssayPlotDefaults(se, number)

Arguments

Details

Parameters available to sample assay plots are:

YAxisSampName:

Integer, which column of se should be shown on the y-axis? Defaults to 1, i.e., the first column. Alternatively, a character field can be supplied containing the name of the column.

YAxisColTable:

Character, what column statistics table should be used to choose a sample to display on the y-axis? Any setting will override YAxisSampName with the selected row in the chosen table upon initialization of the app. Defaults to "---", which means that no table will be used.

Assay:

Integer, which assay should be used to supply the expression values shown on the y-axis? Defaults to 1, i.e., the first assay in se. Alternatively, a string can also be supplied containing the name of the assay, if assays(se) has names.

XAxis:

Character, what variable should be shown on the x-axis? Defaults to "None", but can also be "Row data" or "Sample name".

XAxisRowData:

Character, which column of rowData(se) should be shown on the x-axis if XAxis="Row data"? Defaults to the first entry of rowData(se).

XAxisSampName:

Integer, which column of se should be shown on the x-axis? Defaults to 2 if se contains multiple columns, otherwise it is set to 1. Alternatively, a character field can be supplied containing the name of the column.

XAxisColTable:

Character, what column statistics table should be used to choose a sample to display on the x-axis, if XAxis="Sample name"? Any setting will override XAxisSampName with the selected row in the chosen table upon initialization of the app. Defaults to "---", which means that no table will be used.

All row-based parameters described in ?"iSEE point parameters" are applicable. All plot-based parameters described in ?"iSEE selection parameters" are applicable.

Value

A DataFrame containing default settings for parameters of each of number sample assay panels.

Author(s)

Charlotte Soneson

See Also

?"iSEE point parameters", ?"iSEE selection parameters"

Examples

example(SingleCellExperiment, echo=FALSE) # mock up 'sce'.
sampAssayPlotDefaults(sce, n=1)