R/pairs.bce.R

In BCE: Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data

pairs.bce <- function(x,              # BCE object
                      sample=1,
                      gap=0,
                      upper.panel = NA,
                      diag.panel = NA,
                      ...)
  if (!is.null(attributes(x)$A_not_null)) {
    NextMethod("modMCMC")
  } else {
    
    panel.cor <- function(x, y) text(x=mean(range(x)),y=mean(range(y)),
                                     labels=format(cor(x,y),digits=2))

    panel.hist <- function(x,...) {
      usr <- par("usr")
      on.exit(par(usr))
      par(usr = c(usr[1:2], 0, 2))
      h <- hist(x, plot = FALSE)
      breaks <- h$breaks
      nB <- length(breaks)
      y <- h$counts
      y <- y/max(y)
      rect(breaks[-nB], 0, breaks[-1], y, col = "cyan")

    }
    if (!is.null(upper.panel) && is.na(upper.panel))upper.panel <- panel.cor
    if (!is.null(diag.panel) && is.na(diag.panel))diag.panel <- panel.hist

    ifelse(is.matrix(x$X),X <- t(x$X),X <- t(x$X[sample,,]))      # if only one sample, X is a matrix

    labels <- colnames(X)
    pairs(X, diag.panel =diag.panel, labels = labels,
          gap = gap, upper.panel = upper.panel,...)

  }