R/PlotMixtureUnivariate.R

In antagomir/netresponse: Functional Network Analysis

#' @title Plot univariate mixtures
#' @description Visualize data, centroids and stds for a given univariate Gaussian mixture model with PCA.
#' @param x data vector
#' @param means mode centroids
#' @param sds mode standard deviations
#' @param ws weight for each mode
#' @param title.text Plot title
#' @param xlab.text xlab.text
#' @param ylab.text ylab.text
#' @param binwidth binwidth for histogram
#' @param qofz Mode assignment probabilities for each sample. Samples x modes.
#' @param density.color Color for density lines
#' @param cluster.assignments Vector of cluster indices, indicating cluster for each data point
#' @param ... Further arguments for plot function.
#' @return Used for its side-effects
#' @author Leo Lahti \email{leo.lahti@@iki.fi}
#' @references See citation('netresponse') for citation details.
#' @keywords utilities
#' @examples # plotMixtureUnivariate(dat, means, sds, ws)
PlotMixtureUnivariate <- function(x, means = NULL, sds = NULL, ws = NULL, title.text = NULL, 
    xlab.text = NULL, ylab.text = NULL, binwidth = 0.05, qofz = NULL, density.color = "darkgray", 
    cluster.assignments = NULL, ...) {
    
    # Circumvent warnings
    ..density.. <- NULL
    vals <- NULL
    varname <- NULL
    
    # Find cluster for each sample
    if (is.null(cluster.assignments)) {
        if (is.null(qofz)) {
            qofz <- P.r.s(t(matrix(x)), list(mu = means, sd = sds, w = ws), log = TRUE)
        }
        cluster.assignments <- apply(qofz, 1, which.max)
    }
    
    x <- unname(x)
    df <- data.frame(list(x = x))
    df$mode <- factor(cluster.assignments)
    
    # Histogram and density plot
    pg <- ggplot(df, aes(x = x))
    pg <- pg + geom_histogram(aes(fill = mode), binwidth = binwidth)
    pg <- pg + theme_bw() + xlab(xlab.text) + ylab(ylab.text)
    pg <- pg + ggtitle(title.text)
    
    # If normal mixture parameters are given, overlay Gaussians on top of the plot
    if (!is.null(means)) {
        
        # Estimated normal distributions from the mixture model
        h <- hist(x, seq(min(x) - binwidth - 1/binwidth, max(x) + binwidth + 1/binwidth, 
            binwidth), plot = FALSE)
        df$vals <- seq(min(df$x), max(df$x), length = nrow(df))  # estimation points for fitted Gaussians
        scal <- max(h$counts)/max(ws[[1]] * dnorm(df$vals, mean = means[[1]], sd = sds[[1]]))
        for (comp in seq_len(length(means))) {
            df2 <- data.frame(list(vals = df$vals, varname = scal * ws[[comp]] * 
                dnorm(df$vals, mean = means[[comp]], sd = sds[[comp]])))
            # Add in normal distribution
            pg <- pg + geom_line(aes(x = vals, y = varname), color = density.color, 
                data = df2)
        }
    }
    
    pg
    
}