#Oskar hagberg 2012-04-26
# A function that plots coefficient estimates the LM function
# with 95 % confidence intervals. If sort = TRUEm the effect
# estimates are plotted in P value order.
# By default, singificant estimates get red, but the color can
# be changed by providing another value for signif.
plotCoeff <-
  function(LM,sort = FALSE,signcol = "red"){
    Coeff = summary(LM)$coeff
    if(sort)
      Coeff = Coeff[order(Coeff[,"Pr(>|t|)"]),]
    
    plotidx = row.names(Coeff) != "(Intercept)"
    
    colors = ifelse(Coeff[plotidx,"Pr(>|t|)"]<0.05,signcol,"black")
    tqtile = qt(0.975,LM$df.residual)
    estimate = Coeff[plotidx,"Estimate"]
    leftCI = estimate-tqtile*Coeff[plotidx,"Std. Error"]
    rightCI = estimate+tqtile*Coeff[plotidx,"Std. Error"]
    
    yvals = 1:sum(plotidx)
    
    plot(
      c(leftCI,estimate,rightCI),
      rep(yvals,3),
      axes = FALSE,
      ylab = "",
      xlab = "",
      main = "95 % Confidence Intervals for Coefficient Estimates",
      type = "n"
      )
    grid()
    axis(1)
    
    axis(2,at = yvals,labels = row.names(Coeff)[plotidx],las = 1,tick = FALSE,line =NA)
    
    for(ii in 1:sum(plotidx))
      lines(c(leftCI[ii],rightCI[ii]),c(ii,ii),lwd = 7,col = colors[ii])
    
    
    points(estimate,1:sum(plotidx),pch = 16,col = "white",cex = 1)
  }