R/F_ellipseCoord.R

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

#' A function that returns the coordinates of an ellipse
#'
#' @param a,b,c parameters of the quadratic function a^2x+bx+c
#' @param quadDrop A scalar, fraction of peak height at which to draw
#'  the ellipse
#' @param nPoints an integer, number of points to use to draw the ellipse
#'
#' @return a matrix with x and y coordinates of the ellipse
ellipseCoord = function(a, b, c, quadDrop = 0.95, 
    nPoints = 100) {
    center = -b/(2 * a)
    roots = mapply(a, b, c, FUN = function(A, 
        B, C) {
        Re(polyroot(c(C - log(ifelse(A > 
            0, 1/quadDrop, quadDrop)) + (B^2 - 
            4 * A * C)/(4 * A), B, A))[1])  #Log to go to count scale.
        # Since function is symmetric, does not
        # matter which root we pick, only
        # distance to vertex matters so we just
        # take the first
    })
    anglesEval = seq(0, 2 * pi, length.out = nPoints)
    ab = center - roots
    radii = prod(ab)/sqrt(sin(anglesEval)^2 * 
        ab[1]^2 + ab[2]^2 * cos(anglesEval)^2)
    cbind(x = radii * cos(anglesEval) + center[1], 
        y = radii * sin(anglesEval) + center[2])
}