R/focal.profPlot.R

In butterflyology/ordiBreadth: Ordinated Diet Breadth

focal.profPlot <- function(dat, focal.bug, dist.method = "jaccard", col = c("black", "red")){
  dat.m.f <- dat[-focal.bug, ]
  temp <- which(apply(dat.m.f, 2, sum) == 0)
  if(length(temp) != 0){
    dat.m.f <- dat.m.f[, -temp]
    focal.bug.m.f <- dat[focal.bug, -temp]
      }else{focal.bug.m.f <- dat[focal.bug, ]}
  specialization.m.f <- ordi.breadth(dat.m.f, dist.method = dist.method)
  focal.breadth <- hyp.group.dist.m.f(dat.m.f, grouping = as.numeric(focal.bug.m.f), distances = TRUE)$distances.all
    cols <- rep(col[1], length(focal.breadth))
    cols[which(focal.bug.m.f == 1)] <- col[2]
      specdist <- focal.breadth#[which(focal.bug.m.f==1)]
        cols <- cols[order(specdist)]
        specdisto <- specdist[order(specdist)]
    plot(1:length(cols), specdisto, col = cols, pch = 19, xlab = "", ylab = "distance", las = 1, main = rownames(dat)[focal.bug])
  }