R: Plots helices in arc diagram

Plot Helix Structures {R4RNA}

R Documentation

Plots helices in arc diagram

Description

Plots a helix data frame as an arc diagram, with styling possible with properly named additional columns on the data frame.

Usage

    plotHelix(helix, x = 0, y = 0, flip = FALSE, line = FALSE, arrow = FALSE,
        add = FALSE, shape = "circle", ...)
    plotDoubleHelix(top, bot, line = TRUE, arrow = FALSE, add = FALSE, ...)
    plotOverlapHelix(predict, known, miss = "black", line = TRUE,
        arrow = FALSE, add = FALSE, overlap.cutoff = 1, ...)
    plotArcs(i, j, length, x = 0, y = 0, flip = FALSE, shape = "circle", ...)
    plotArc(i, j, x = 0, y = 0, flip = FALSE, shape = "circle", ...)

Arguments

`helix, top, bot, predict, known`	Helix data.frames, with the four mandatory columns. Any other column will be considered a styling column, and will be used for styling the helix. See `example` for styling usage. See `Details` for exact usage of each helix.
`x, y`	The coordinate of the left bottom corner of the plot, useful for manually positioning figure elements.
`flip`	If TRUE, flips the arcs upside down about the y-axis.
`line`	If TRUE, a horizontal line representing the sequence is plotted.
`arrow`	If TRUE, an arrow is played on the right end of the line.
`add`	If TRUE, graphical elements are added to the active plot device, else a new plot device is created for the plot.
`shape`	One of "circle", "triangle", or "square", specifying the shape of the arcs.
`miss`	The colour for unpredicted arcs in overlapping diagrams, see `details` for more information.
`overlap.cutoff`	Decimal between 0 and 1 indicating the percentage of basepairs within a helix that have to be overlapping for the entire helix to count as overlapping. Default is 1, or 100
`i, j`	The starting and ending position of the arc along the x-axis
`length`	The total number of arcs to draw by incrementing i and decrementing j. Used to draw helices.
`...`	Any additional parameters passed to `par`

Details

plotHelix creates a arc diagram with all arcs on top, plotDoubleHelix creates a diagram with arcs on the top and bottom. plotOverlapHelix is slight trickier, and given two structures predict and known, plots the predicted helices that are known on top, predicted helices that are not known on the bottom, and finally plots unpredicted helices on top in the colour defined by miss.

plotArc and plotArcs are the core functions that make everything work, and may be used for extreme fine-tuning and customization.

Value

Not intended to return a value, will plot to GUI or file if specific.

Author(s)

Daniel Lai

Examples

    data(helix)

    # Plot helix plain
    plotHelix(known)

    # Apply global appearance options
    plotHelix(known, line = TRUE, arrow = TRUE, col = "blue", lwd = 1.5)

    # Add extra column with styling options
    known$lty <- 1:4
    known$lwd <- 1:2
    known$col <- c(rgb(1, 0, 0), "orange", "yellow", "#00FF00", 4, "purple")
    plotHelix(known)

    # Manually colour helices according to value
    helix$col <- "red"
    helix$col[which(helix$value < 1e-3)] <- "orange"
    helix$col[which(helix$value < 1e-4)] <- "green"
    helix$col[which(helix$value < 1e-5)] <- "blue"
    plotHelix(helix)

    # Automatically creating a similar plot with legend
    coloured <- colourByValue(helix, log = TRUE, get = TRUE)
    plotHelix(coloured, line = TRUE, arrow = TRUE)
    legend("topleft", legend = attr(coloured, "legend"),
        fill = attr(coloured, "fill"), title = "P-value", text.col = "black")    

    # Plot both helices with styles
    plotDoubleHelix(helix, known)

    # Overlap helix
    plotOverlapHelix(helix, known)

[Package R4RNA version 1.8.0 Index]