iSEE (version 0.98.2)

defaults: Parameter defaults

Description

Create default settings for various panels in the iSEE interface.

Usage

redDimPlotDefaults(se, number)
geneExprPlotDefaults(se, number)
colDataPlotDefaults(se, number)
geneStatTableDefaults(se, number)

Arguments

se

A SingleCellExperiment object.

number

An integer scalar, specifying the maximum number of panels of the corresponding type that can be added to the interface.

Value

A DataFrame containing default settings for various parameters of each panel.

Reduced dimension plot parameters

Type:

Integer, which entry of reducedDims(se) should be shown? Defaults to 1, i.e., the first entry. We use an index rather than the name, as the latter may not be unique.

XAxis:

Integer, which component should be shown on the x-axis? Defaults to 1.

YAxis:

Integer, which component should be shown on the y-axis? Defaults to 2.

Gene expression plot parameters

GeneTable:

Character, what gene statistic table should be used to choose a gene to display on the y-axis? Defaults to an empty string, which means that the first available 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. We use an index rather than the name, as the latter may not be unique.

XAxis:

Character, what variable should be shown on the x-axis? Defaults to "None".

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).

XAxisGeneText:

Character, which gene's expression should be shown on the x-axis if XAxis="Gene text"? Defaults to the name of the first row in se, using expression values specified in Assay.

XAxisGeneTable:

Character, which gene statistic table should be used to choose a gene to put on the x-axis if XAxis="Gene table"? Defaults to an empty string, which means that the first available table will be used.

Column data plot parameters

YAxisColData:

Character, which column of colData(se) should be shown on the y-axis? Defaults to the first entry of colData(se).

XAxis:

Character, what variable should be shown on the x-axis? Defaults to "None".

XAxisColData:

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

Coloring parameters

ColorPanelOpen:

Logical, should the color parameter panel be open upon initialization? Defaults to FALSE.

ColorBy:

Character, what type of data should be used for coloring? Defaults to "None".

ColorByColData:

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

ColorByGeneTable:

Character, which gene statistic table should be used to choose a gene to color by, if ColorBy="Gene table"? Defaults to an empty string, which means that the first available table will be used.

ColorByGeneTableAssay:

Integer, which assay should be used to supply the expression values for colouring if ColorBy="Gene table"? Defaults to 1, i.e., the first assay in se.

ColorByGeneText:

Character, which gene should be used to choose a gene to color by, if ColorBy="Gene text"? Defaults to an empty string, which means that the first available table will be used.

ColorByGeneTextAssay:

Integer, which assay should be used to supply the expression values for colouring if ColorBy="Gene text"? Defaults to 1, i.e., the first assay in se.

Brushing parameters

BrushPanelOpen:

Logical, should the brushing parameter panel be open upon initialization? Defaults to FALSE.

BrushByPlot:

Character, which other plot should be used for point selection in the current plot? Defaults to an empty string, which means that no plot is used for point selection.

BrushEffect:

Character, what is the effect of receiving a brush input? Can be "Restrict", where only the brushed points are shown; "Color", where the brushed points have a different color; or "Transparent", where all points other than the brushed points are made transparent. Defaults to "Transparent".

BrushColor:

Character, what color should be used for the brushed points when BrushEffect="Color"? Defaults to "red".

BrushAlpha:

Numeric, what level of transparency should be used for the unbrushed points whe BrushEffect="Transparent"? This should lie in [0, 1], where 0 is fully transparent and 1 is fully opaque. Defaults to 0.1.

Other plot parameters

PlotPanelOpen:

Logical, should the plot parameter panel be open upon initialization? Defaults to FALSE.

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.

Gene statistic table parameters

Selected:

Integer, containing the index of the row to be initially selected. Defaults to the first row, i.e., 1.

Search:

Character, containing the initial value of the search field. Defaults to an empty string.

SearchColumns:

A list containing character vectors of length equal to the number of columns in rowData(se), specifying the initial value of the search field for each column. All entries default to an empty string.

Examples

# NOT RUN {
library(scRNAseq)
data(allen)
class(allen)

library(scater)
sce <- as(allen, "SingleCellExperiment")
counts(sce) <- assay(sce, "tophat_counts")
sce <- normalize(sce)
sce <- runPCA(sce)
sce

redDimPlotDefaults(sce, number=5)
geneExprPlotDefaults(sce, number=5)
colDataPlotDefaults(sce, number=5)
geneStatTableDefaults(sce, number=5)
# }