ColumnDataTable-class: The ColumnDataTable panel

In iSEE: Interactive SummarizedExperiment Explorer

Description

The ColumnDataTable is a panel class for creating a ColumnTable where the value of the table is defined as the colData of the SummarizedExperiment. It provides functionality to extract the colData to coerce it into an appropriate data.frame in preparation for rendering.

Slot overview

This class inherits all slots from its parent ColumnTable and Table classes.

Constructor

ColumnDataTable(...) creates an instance of a ColumnDataTable class, where any slot and its value can be passed to ... as a named argument.

Note that ColSearch should be a character vector of length equal to the total number of columns in the colData, though only the entries for the atomic fields will actually be used.

Supported methods

In the following code snippets, x is an instance of a ColumnDataTable class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "ColumnDataTable" entry containing valid.colData.names, a character vector of names of atomic columns of the colData. This will also call the equivalent ColumnTable method.

• .refineParameters(x, se) adjusts ColSearch to a character vector of length equal to the number of atomic fields in the colData. This will also call the equivalent ColumnTable method for further refinements to x.

For defining the interface:

• .fullName(x) will return "Column data table".

• .panelColor(x) will return the specified default color for this panel class.

For creating the output:

• .generateTable(x, envir) will modify envir to contain the relevant data.frame for display, while returning a character vector of commands required to produce that data.frame. Each row of the data.frame should correspond to a column of the SummarizedExperiment.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a panel-specific tour.

Unless explicitly specialized above, all methods from the parent class Panel are also available.

Author(s)

Aaron Lun

Examples

#################
# For end-users #
#################

x <- ColumnDataTable()
x[["Selected"]]
x[["Selected"]] <- "SOME_SAMPLE_NAME"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()

# Search column refinement works as expected.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

iSEE documentation built on Feb. 3, 2021, 2:01 a.m.