covPlotly-class: Container for plotly-based coverage plots

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

Container for plotly-based coverage plots

Description

A covPlotly object is created when plotView is called using a covPlotObject as input. It stores metadata alongside the plotly object, which allows it to be drawn at various resolutions. Smaller resolutions lead to faster draws at expense of more jagged plots.

Usage

## S4 method for signature 'covPlotly'
getExonRanges(object)

## S4 method for signature 'covPlotly'
setResolution(object, resolution)

## S4 method for signature 'covPlotly'
showExons(object)

Arguments

object	A covPlotly object
resolution	How many horizontal pixels of resolution should be shown in the final plotly object. Set to 0 to disable.

Value

For show(): A plotly object synthesised by plotView() For getExonRanges(): A named GRanges object containing exon ranges For showExons(): A named GRanges object containing exon ranges, and additionally "shows" the plotly coverage plot with annotation replaced by named exons For setResolution() Returns the covPlotly object with addition of resolution set by the corresponding parameter. When show() is called, the plotly object with the new coverage resolution will be displayed.

Functions

• getExonRanges(covPlotly): Returns a named GRanges object containing exon ranges, without showing the associated plotly object

• setResolution(covPlotly): Returns a covPlotly object after setting the output resolution of the plotly-based coverage plots.

• showExons(covPlotly): Returns a named GRanges object containing exon ranges, and shows the plotly object with the annotation track showing the named exons

See Also

plotView

Examples

se <- SpliceWiz_example_NxtSE(novelSplicing = TRUE)

# Assign annotation of the experimental conditions
colData(se)$treatment <- rep(c("A", "B"), each = 3)

# Retrieve coverage data for all samples for the gene "SRSF3" (and surrounds)

dataObj <- getCoverageData(
    se,
    Gene = "SRSF3",
    tracks = colnames(se)
)

plotObj_samples <- getPlotObject(
    dataObj,
    Event = "SE:SRSF3-203-exon4;SRSF3-202-int3"
)

if(interactive()) {

    # Create covPlotly object by setting `usePlotly = TRUE`
    p <- plotView(plotObj_samples, usePlotly = TRUE)

    # Display plotly plot
    show(p)

    # Set resolution to 2000; display new plot
    p <- setResolution(p, resolution = 2000)
    show(p)

    # Display exon annotation along with generated plot;
    # - also returns GRanges object
    gr <- showExons(p)
}

alexchwong/SpliceWiz documentation built on March 17, 2024, 3:16 a.m.