LoopCircos-class {RPointCloud}

The LoopCircos Class

Description

A LoopCircos object represents a one-dimensional cycle (a loop, or topogical eequivalent of a circle), along with a set of features that vary around the loop and can be plotted in a "circos" plot to help explain why the loop exists. The LoopCircos class inherits from the Cycle class, so you can think of it as a cycle object with extra information (namely, the explanatory features).

Usage

LoopCircos(cycle, angles, colors)
angleMeans(view, rips, cycle = NULL, dset, angleWidth = 20, incr = 15)
## S4 method for signature 'LoopCircos'
image(x, na.col = "grey", ...)

Arguments

cycle

In the LoopCircos function, an object of the Cycle class. In the angleMeans function, an object of the Cycle class.

angles

A matrix where columns are features, rows are angles, and the value is the mean expression of that feature in a sector around that central angle. These are almost always constructed using the angleMeans function.

colors

A list of character vectors, each of length two, containing the names or hexadecimal representations of colors used to create a color ramp to display the feature. The list should be the same length as the number of features to be displayed.

view

A (layout) matrix with coordinates showing where to plot each point in the feature while computing means in sectors.

rips

A Rips diagram object.

dset

The numeric matrix from which Featuers are drawn.

angleWidth

A numeric vector of length one; the width (in degrees) of each sector.

incr

A numeric vector; the increment (in degeres) between sector centers.

x

A LoopCircos object.

na.col

A character string; the color in which to plot missing (NA) data.

...

The usual set of additional graphical parameters.

Value

The angleMeans function computes the mean expression of each numeric feature in a two-dimensional sector swept out around the centroid of the support of a cycle. It returns these values as a matrix, with each row corresponding to the angle (in degrees) around the centroid of the cycle.

The LoopCircos function constructs and returns an object of the LoopCircos class

The image method returns (invisibly) the LoopCircos object that was its first argument.

Slots

angles:

A matrix of angle means.

colors:

A list of color-pairs for displayign features.

Methods

image(x, ...):

Produce a circos plot of a LoopCircos object.

Author(s)

Kevin R. Coombes <[e-mail]>

See Also

Cycle, LoopFeature, ripsDiag

Examples

data(CLL)
cyc1 <- Cycle(ripdiag, 1, 236, "forestgreen")
V <- cmdscale(daisydist)
poof <- angleMeans(V, ripdiag, cyc1, clinical)
poof[is.na(poof)] <- 0
angle.df <- poof[, c("mutation.status", "CatCD38", "CatB2M", "CatRAI",
                     "Massive.Splenomegaly", "Hypogammaglobulinemia")]
colorScheme <- list(c(M = "green", U = "magenta"),
                    c(Hi = "cyan", Lo ="red"),
                    c(Hi = "blue", Lo = "yellow"),
                    c(Hi = "#dddddd", Lo = "#111111"),
                    c(No = "#dddddd", Yes = "brown"),
                    c(No = "#dddddd", Yes = "purple"))
annote <- LoopCircos(cyc1, angle.df, colorScheme)
image(annote)