defaults {iSEE} | R Documentation |
Create default settings for various panels in the iSEE interface.
redDimPlotDefaults(se, number) featAssayPlotDefaults(se, number) colDataPlotDefaults(se, number) rowStatTableDefaults(se, number) rowDataPlotDefaults(se, number) heatMapPlotDefaults(se, number)
se |
A SummarizedExperiment object. |
number |
An integer scalar, specifying the maximum number of panels of the corresponding type that can be added to the interface. |
A DataFrame containing default settings for various parameters of each panel.
Type
:Integer, which entry of reducedDims(se)
should be shown?
Defaults to 1, i.e., the first entry.
Alternatively, a string can be supplied containing the name of the reduced dimension field, if reducedDims(se)
has names.
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.
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 statistic table should be used to choose a feature to display on the y-axis?
Any setting will override YAxisFeatName
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
upon initialization of the app.
Defaults to "---"
, which means that no table will be used.
YAxis
:Character, which column of colData(se)
should be shown on the y-axis?
Defaults to the first entry of colData(se)
.
XAxis
:Character, what type of variable should be shown on the x-axis?
Defaults to "None"
, but can also be "Column data"
.
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)
.
YAxis
:Character, which column of rowData(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"
, but can also be "Row table"
, "Row data"
or "Feature 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)
.
ColorBy
:Character, what type of data should be used for coloring?
Defaults to "None"
, but can also be "Row table"
, "Feature name"
or "Column data"
.
ColorByDefaultColor
:String specifying the default point colour when ColorBy="None"
.
Defaults to "black"
.
ColorByFeatName
:Integer, the index of the feature to use for colouring based on expression, 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.
ColorByRowTable
:Character, which row statistic table should be used to choose a feature to color by, if ColorBy="Feature name"
?
Any setting will override ColorByFeatName
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.
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 from the text if ColorBy="Feature name"
.
Defaults to "red"
.
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"
and "Other"
.
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.
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.
Selected
:Integer, containing the index of the row to be initially selected. Defaults to the first row, i.e., 1. Alternatively, a string can be supplied containing the row name.
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.
The features/rows to be used in the construction of the heatmap are specified with:
FeatName
:List of length equal to the number of panels.
Each list entry corresponds to a panel and should be an integer vector with the indices of the feature(s) for which to show the expression in the heatmap.
Defaults to 1L
for each panel, i.e., the first feature in se
.
Alternatively, a character vector can be supplied containing the names of the features.
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.
FeatNameSource
:Character, which other panel should be used to choose the features to show in the heatmap?
Defaults to "---"
, which means that no panel is used for feature selection.
FeatNameBoxOpen
:Logical, should the feature selection box be open upon initialization?
Defaults to FALSE
.
The column metadata variables control the ordering of the samples in the heatmap. They can be controlled with:
ColData
:List of length equal to the number of panels.
Each list entry corresponds to a panel and should contain a character vector specifying the field(s) of colData(se)
that should be used to order the samples in the heatmap.
Note that these fields will also appear as annotation bars.
Each character vector defaults to the first entry of colData(se)
.
ColDataBoxOpen
:Logical, should the column data selection box be open upon initialization?
Defaults to FALSE
.
A variety of parameters are available to control the color scale of the heatmap. They can be specified with:
ColorBoxOpen
:Logical, should the color selection panel for the heatmap be open upon initialization?
Defaults to FALSE
.
CenterScale
:List of length equal to the number of panels.
Each list entry corresponds to a panel and contains a character vector specifying whether each row of expression values should be mean-centered and/or scaled to unit variance.
Defaults to "Centered"
.
Users can set it to c("Centered", "Scaled")
to obtain mean-centered and unit-scaled rows.
Lower
:Numeric, what should be the lower bound of the color scale for the values in the heatmap? All values below this threshold will be shown in the same color. Defaults to -Inf, meaning that the lowest value in the data matrix will be used.
Upper
:Numeric, what should be the upper bound of the color scale for the values in the heatmap? All values above this threshold will be shown in the same color. Defaults to Inf, meaning that the highest value in the data matrix will be used.
ColorScale
:Character, what color scale (in the form low-mid-high) should be used to color the heatmap when values are centered?
Defaults to "purple-black-yellow"
.
Finally, the ZoomData
field for heatmaps should contain an integer vector of consecutive indices to zoom into from the full heatmap.
This vector will subset the entries in FeatName
for a given panel.
This defaults to NULL
, i.e., all specified features in FeatName
are shown.
For the point-based plots, the following options apply:
SelectBoxOpen
:Logical, should the point selection parameter box be open upon initialization?
Defaults to FALSE
.
SelectByPlot
:Character, which other plot should be used for point selection in the current plot?
Defaults to "---"
, which means that no plot is used for point selection.
SelectEffect
:Character, what is the effect of receiving point selection information?
Can be "Restrict"
, where only the selected points are shown; "Color"
, where the selected points have a different color;
or "Transparent"
, where all points other than those selected are made transparent.
Defaults to "Transparent"
.
SelectColor
:Character, what color should be used for the selected points when SelectEffect="Color"
?
Defaults to "red"
.
SelectAlpha
:Numeric, what level of transparency should be used for the unselected points when SelectEffect="Transparent"
?
This should lie in [0, 1], where 0 is fully transparent and 1 is fully opaque.
Defaults to 0.1.
Note that point selection cannot occur between row data plots and the other plot types. This is because each point in a row data plot is a feature, while each point represents a sample in the other plots. Point selection can only occur between plots of the same point type.
For the row statistics tables, the following options apply:
SelectBoxOpen
:Logical, should the point selection parameter box be open upon initialization?
Defaults to FALSE
.
SelectByPlot
:Character, which other plot should be used to select features in the current table?
Defaults to "---"
, which means that no plot is used for point selection.
Only row data plots can be used for selecting points to supply to tables.
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) featAssayPlotDefaults(sce, number=5) colDataPlotDefaults(sce, number=5) rowStatTableDefaults(sce, number=5) rowDataPlotDefaults(sce, number=5) heatMapPlotDefaults(sce, number=5)