featAssayPlotDefaults {iSEE}R Documentation

Feature assay plot defaults

Description

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

Usage

featAssayPlotDefaults(se, number)

Arguments

se

A SummarizedExperiment object.

number

An integer scalar, specifying the maximum number of feature assay plots that can be added to the interface.

Details

Parameters available to feature assay plots are:

YAxisFeatName:

Integer, the index of the feature for which to show the expression on the y-axis if YAxis="Feature name". Defaults to 1, i.e., the first feature in se. Alternatively, a string can be supplied containing the name of the feature, i.e., the row name.

YAxisRowTable:

Character, what row statistics table should be used to choose a feature to display on the y-axis? Any setting will override YAxisFeatName 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 type of variable should be shown on the x-axis? Defaults to "None", but can also be "Row table", "Column data" or "Feature name".

XAxisColData:

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

XAxisFeatName:

Integer, the index of the feature for which to show the expression on the x-axis if XAxis="Feature name". Defaults to 1, i.e., the first feature in se. Alternatively, a string can be supplied containing the name of the feature.

XAxisRowTable:

Character, which row statistic table should be used to choose a feature to put on the x-axis if XAxis="Row table"? Any setting will override XAxisFeatName with the selected row in the chosen table upon initialization of the app. Defaults to "---", which means that no table will be used.

All column-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 feature assay panels.

Author(s)

Aaron Lun

See Also

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

Examples

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

[Package iSEE version 1.2.4 Index]