iSEE point parameters {iSEE}R Documentation

Point plot aesthetic parameters

Description

Parameters related to aesthetics for point-based plotting panels.

Coloring parameters

ColorBy:

Character, what type of data should be used for coloring? Defaults to "None", but can also be "Feature name", "Sample name", or "Column data" (for column-based plots) or "Row data" for (row-based plots).

ColorByDefaultColor:

String specifying the default point colour when ColorBy="None". Defaults to "black".

ColorByFeatName:

Integer, the index of the feature to use if ColorBy="Feature name". Defaults to 1, i.e., the first feature in se. Alternatively, a string can be supplied containing the name of the feature.

ColorBySampName:

Integer, the index of the sample to use if ColorBy="Sample name". Defaults to 1, i.e., the first sample in se. Alternatively, a string can be supplied containing the name of the sample.

ColorByRowTable:

Character, which row statistics table should be used to choose a feature to color by, if ColorBy="Feature name"? Any setting will override ColorByFeatName with the selected row in the chosen table upon initialization of the app. Defaults to "---", which means that no table will be used.

ColorByColTable:

Character, which column statistics table should be used to choose a sample to color by, if ColorBy="Sample name"? Any setting will override ColorBySampName with the selected row in the chosen table upon initialization of the app. Defaults to "---", which means that no table will be used.

For the plots where each point represents a sample (i.e., all plots except for heatmaps and row data plots), the following additional options apply:

ColorByColData:

Character, which column of colData(se) should be used for colouring if ColorBy="Column data"? Defaults to the first entry of colData(se).

ColorByFeatNameAssay:

Integer, which assay should be used to supply the expression values for colouring if ColorBy="Feature name"? 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.

ColorBySampNameColor:

String specifying the colour to be used to highlight the selected sample if ColorBy="Sample name". Defaults to "red".

For plots where each point represents a feature (i.e., row data plots), the following additional options apply:

ColorByRowData:

Character, which column of rowData(se) should be used for colouring if ColorBy="Row data"? Defaults to the first entry of rowData(se).

ColorByFeatNameColor:

String specifying the colour to be used to highlight the selected feature if ColorBy="Feature name". Defaults to "red".

ColorBySampNameAssay:

Integer, which assay should be used to supply the expression values for colouring if ColorBy="Sample name"? 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.

Shape parameters

ShapeBy:

Character, what type of data should be used for controlling shape? Defaults to "None", but can also be "Column data".

For the plots where each point represents a sample (i.e., all plots except for heatmaps and row data plots), the following additional options apply:

ShapeByColData:

Character, which column of colData(se) should be used for shaping if ShapeBy="Column data"? This should refer to a categorical variable, and will default to the first such entry of colData(se).

For plots where each point represents a feature (i.e., row data plots), the following additional options apply:

ShapeByRowData:

Character, which column of rowData(se) should be used for shaping if ShapeBy="Row data"? This should refer to a categorical variable, and will default to the first such entry of rowData(se).

Contour line parameters

ContourAdd:

Logical, should contour lines be added to the plot?

ContourColor:

String specifying the default colour of contour lines.

Faceting parameters

FacetByRow:

Logical indicating whether the plot should be faceted by row.

FacetByColumn:

Logical indicating whether the plot should be faceted by row.

For the plots where each point represents a sample (i.e., all plots except for heatmaps and row data plots), the following additional options apply:

RowFacetByColData:

Character, which column of colData(se) should be used to facet by row? This should refer to a categorical variable, and will default to the first such entry of colData(se).

ColumnFacetByColData:

Character, which column of colData(se) should be used to facet by column? This should refer to a categorical variable, and will default to the first such entry of colData(se).

For the plots where each point represents a feature (i.e., row data plots), the following additional options apply:

RowFacetByRowData:

Character, which column of colData(se) should be used to facet by row? This should refer to a categorical variable, and will default to the first such entry of colData(se).

ColumnFacetByRowData:

Character, which column of colData(se) should be used to facet by column? This should refer to a categorical variable, and will default to the first such entry of colData(se).

Other plot parameters

Parameter visibility options are:

DataBoxOpen:

Logical, should the data parameter box be open upon initialization? Defaults to FALSE.

VisualBoxOpen:

Logical, should the visual parameter box be open upon initialization? Defaults to FALSE.

VisualChoices:

A list containing one character vector, specifying the visual box parameters to be shown upon initialization. This defaults to list("Color") to show only the coloring parameters, but the internal vector can also contain "Points", "Facets" and "Other".

Options related to the appearance of points are:

PointSize:

Numeric, the size of the points. Defaults to 1.

PointAlpha:

Numeric, what level of transparency should be used for the points? Ignored when SelectEffect="Transparent" and the transmitting plot has a non-NULL selection of points. Defaults to 1.

Downsample:

Logical, indicating whether downsampling of overlapping points should be performed. Defaults to FALSE.

SampleRes:

Numeric, specifying the downsampling resolution, i.e., the granularity at which points are considered to overlap. Higher values result in a more stringent definition of overlaps, and thus less downsampling. Defaults to 200.

Text-related parameters are:

FontSize:

Numeric, size of the font. Defaults to 1.

LegendPosition:

String specifying the legend position. Defaults to "Bottom" but can also be "Right".

ZoomData:

A list containing numeric vectors of length 4, containing values with names "xmin", "xmax", "ymin" and "ymax". These define the zoom window on the x- and y-axes. Each element of the list defaults to NULL, i.e., no zooming is performed.

Author(s)

Aaron Lun, Kevin Rue-Albrecht, Charlotte Soneson

See Also

redDimPlotDefaults, featAssayPlotDefaults, colDataPlotDefaults, rowDataPlotDefaults, sampAssayPlotDefaults

Examples

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

[Package iSEE version 1.2.4 Index]