iSEEOptions: Global 'iSEE' options
In iSEE: Interactive SummarizedExperiment Explorer

Description Usage Format Commands Available options Comments on globals Author(s) Examples

Get or set global values that are used by relevant panels during construction and application initialization. This allows users to easily modify parameters for multiple panels simultaneously.

1	iSEEOptions

An object of class list of length 4.

str(iSEEOptions$get()) will show the default values for all options.

iSEEOptions$set(name=value) will set the named option to value.

iSEEOptions$restore() will reset the global options to the package default values.

point.color: Default color of data points in DotPlot panels (character).
point.size: Default size of data points in DotPlot panels (numeric).
point.alpha: Default alpha level controlling transparency of data points in DotPlot panels (numeric).
downsample: Enable visual downsampling in DotPlot panels (logical).
downsample.resolution: Resolution of the visual downsampling, if active (numeric).
selected.color: Color of selected data points in DotPlot panels (character).
selected.alpha: Alpha level controlling transparency of data points not selected in DotPlot panels (numeric).
selection.dynamic.single: Toggle dynamic single selections for all panels (logical).
selection.dynamic.multiple: Toggle dynamic multiple selections for all panels (logical).
contour.color: Color of the 2d density estimation contour in DotPlot panels (character).
font.size: Global multiplier controlling the magnification of plot title and text elements in DotPlot panels (numeric).
legend.position: Position of the legend in DotPlot and ComplexHeatmapPlot panels (one of "Bottom", "Right").
legend.direction: Position of the legend in DotPlot and ComplexHeatmapPlot panels (one of "Horizontal", "Vertical").
panel.width: Default panel grid width (must be between 1 and 12).
panel.height: Default panel height (in pixels).
panel.color: Named character vector of colors. The names of the vector should be set to the name of class to be overridden; if a class is not named here, its default color is used. It is highly recommended to define colors as hex color codes (e.g., "#1e90ff"), for full compatibility with both HTML elements and R plots.
color.maxlevels: Maximum number of levels for a categorical variable used for coloring. Variables with more levels are coerced to numeric to avoid problems with an overly-large legend. Defaults to 24.
factor.maxlevels: Maximum number of levels for a categorical variable to be used anywhere in the app. Variables with more levels are coerced to numeric to avoid rendering delays. Defaults to 100.
assay: Character vector of assay names to use if available, in order of preference.
RowTable.select.details: A function that takes a string containing the name of a feature (i.e., the current selection in the RowTable) and returns a HTML element with more details.
ColumnTable.select.details: A function that takes a string containing the name of a sample (i.e., the current selection in the ColumnTable) and returns a HTML element with more details.

As much as possible, these options will only affect the application during Panel construction. This enables users to reproduce the app state from one session to another by simply saving the memory. Otherwise, users would also have to export the state of the global variables to properly recapitulate the app state.

For developers: following this guideline generally means that the globals should reflect some parameter that is already present as a formal slot in the panel class. If all panels must have the same value, this can be enforced via some creative use of .cacheCommonInfo (to cache the first encountered value of the global slot) followed by .refineParameters (to enforce that value on every other panel of the same class) - see the MAPlot class in the iSEEu package for a working example.

Kevin Rue-Albrecht