FeatureAssayPlot-class: The FeatureAssayPlot panel

Description Slot overview Constructor Supported methods Author(s) See Also Examples

Description

The FeatureAssayPlot is a panel class for creating a ColumnDotPlot where the y-axis represents the expression of a feature of interest, using the assay values of the SummarizedExperiment. It provides slots and methods to specify the feature and what to plot on the x-axis, as well as a method to actually create a data.frame containing those pieces of data in preparation for plotting.

Slot overview

The following slots control the values on the y-axis:

The following slots control the values on the x-axis:

In addition, this class inherits all slots from its parent ColumnDotPlot, DotPlot and Panel classes.

Constructor

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

Supported methods

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

For setting up data values:

For defining the interface:

For monitoring reactive expressions:

For defining the panel name:

For creating the plot:

For managing selections:

For documentation:

Author(s)

Aaron Lun

See Also

ColumnDotPlot, for the immediate parent class.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
#################
# For end-users #
#################

x <- FeatureAssayPlot()
x[["XAxis"]]
x[["Assay"]] <- "logcounts"
x[["XAxisColumnData"]] <- "stuff"

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

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

old_assay_names <- assayNames(sce)
assayNames(sce) <- character(length(old_assay_names))

# Spits out a NULL and a warning if no assays are named.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
assayNames(sce) <- old_assay_names
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

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