| RowDataPlot-class {iSEE} | R Documentation |
The RowDataPlot is a panel class for creating a RowDotPlot where the y-axis represents a variable from the rowData of a SummarizedExperiment object.
It provides slots and methods for specifying which row metadata variable to use and what to plot on the x-axis.
The following slots control the dimensionality reduction result that is used:
YAxis, a string specifying the row of the rowData to show on the y-axis.
If NA, defaults to the first valid field (see ?".refineParameters,RowDotPlot-method").
XAxis, string specifying what should be plotting on the x-axis.
This can be any one of "None" or "Row data".
Defaults to "None".
XAxisRowData, string specifying the row of the rowData to show on the x-axis.
If NA, defaults to the first valid field.
In addition, this class inherits all slots from its parent RowDotPlot, DotPlot and Panel classes.
RowDataPlot(...) creates an instance of a RowDataPlot class, where any slot and its value can be passed to ... as a named argument.
In the following code snippets, x is an instance of a RowDataPlot class.
Refer to the documentation for each method for more details on the remaining arguments.
For setting up data values:
.refineParameters(x, se) returns x after replacing any NA value in YAxis or XAxisRowData with the name of the first valid rowData variable.
This will also call the equivalent RowDotPlot method for further refinements to x.
If no valid row metadata variables are available, NULL is returned instead.
For defining the interface:
.defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.
.panelColor(x) will return the specified default color for this panel class.
.allowableXAxisChoices(x, se) returns a character vector specifying the acceptable variables in rowData(se) that can be used as choices for the x-axis.
.allowableYAxisChoices(x, se) returns a character vector specifying the acceptable variables in rowData(se) that can be used as choices for the y-axis.
For monitoring reactive expressions:
.createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes.
This will also call the equivalent RowDotPlot method.
For defining the panel name:
.fullName(x) will return "Row data plot".
For creating the plot:
.generateDotPlotData(x, envir) will create a data.frame of row metadata variables in envir.
It will return the commands required to do so as well as a list of labels.
Subclasses do not have to provide any methods, as this is a concrete class.
Aaron Lun
RowDotPlot, for the immediate parent class.
################# # For end-users # ################# x <- RowDataPlot() x[["XAxis"]] x[["XAxis"]] <- "Row data" ################## # For developers # ################## library(scater) sce <- mockSCE() sce <- logNormCounts(sce) # Spits out a NULL and a warning if is nothing to plot. sce0 <- .cacheCommonInfo(x, sce) .refineParameters(x, sce0) # Replaces the default with something sensible. rowData(sce)$Stuff <- runif(nrow(sce)) sce0 <- .cacheCommonInfo(x, sce) .refineParameters(x, sce0)