95% Confidence Interval

Variation

Use

To see the 95 percent confidence interval of the mean
To combine it with the Box and Whisker plot's whiskers and outliers

Arguments

points.x: - All X values of points that will be plotted
points.y: - All Y values of points that will be plotted
distribution: - Defines what method to use when calculating the interval. Choices are "t" and "normal".
y.limits: - Needs to be supplied the limits of the Y data. Can be derived within panel due to having another panel with different limits.
ci95.ghost: - What percentage of opacity should be used. 1 being solid, 0 be 'invisible'
whiskers.and.outliers: - Logical. Decides whether or not to plot the whiskers and circle the outliers.

Notes

Explaination of the graphic (from middle out)
- Center large dot - Mean
- Bold/thick lines
  - 95% Confidence Interval of the mean
  - Stops near the Mean Dot as to not overlap
  - Does include the interval inbetween the two lines
- Thin lines - The 'whisker' part of Box and Whisker plot. (The boxes are set to be transparent.)
- Circles - Outliers
- N = ## - Number of points used
Due to the 'ci95.ghost', this panel function may be place almost anywhere.
The rounded ends from the confidence interval are due to the defaults in Lattice that could not be changed.
If you do not like the 'N=##' at the bottom. Remove it in the code.

Code

'plot.ci95.whisker' <- 
function(
  points.x = x, 
  points.y = y, 
  distribution = "t", #"normal"
  y.limits = NULL,
  ci95.ghost = 1,
  whiskers.and.outliers = FALSE
){
cat("\nPlotting 95% Confidence Interval\n")
  
  if(is.null(y.limits)) stop("\n\n\ty.limits was not supplied\n\n")

  y.split <- split(points.y,points.x)
  x.locations <- as.numeric(names(y.split))

  for( i in x.locations){
    x <- i    
    y <- y.split[[as.character(x)]]
    a <- mean(y)
    s <- sd(y)
    n <- length(y)
    if(distribution == "t") error <- qt(0.975,df=n-1)*s/sqrt(n)
    if(distribution == "normal") error <- qnorm(0.975)*s/sqrt(n)
    
    top.ci <- a + error
    bot.ci <- a - error

    ### Plot Lower Interval
    lsegments(
      x0 = x,  # X Start
      y0 = bot.ci,  #Y Start
      x1 = x,  # X Finish
      y1 = min(a,c(a - 0.02*diff(y.limits))),  # Y Finish, with 2% buffer away from center point (creates white space)
      col = "black",
      lty = 1,
      lwd = 8,
      alpha = .25
    )
    
    ### Plot Upper Interval
    lsegments(
      x0 = x,
      y0 = top.ci,
      x1 = x,
      y1 = max(a,c(a + 0.02*diff(y.limits))),
      col = "black",
      lty = 1,
      lwd = 8,
      alpha = .25
    )
    
    ### Plot Mean Dot
    lpoints(
      x = x, 
      y = a,
      pch = 16, # Solid Circle
      col = "black",
      cex = .75,
      alpha = ci95.ghost
    )

    ### Write how many points there are at the bottom
    ltext(
      x = x,
      y = c(y.limits[1]-diff(y.limits)*0),  # To have the text written in the 3% buffer
      offset = 0,
      labels = c(paste("N =",n,sep=" ",collapse="")),
      cex = .5,
      srt = 90,  # Rotate text 90 degrees
    )

    
    ### Make Box Plot Box Color Transparent
    box.rectangle <- trellis.par.get("box.rectangle")
    box.rectangle$col <- "transparent"
    trellis.par.set("box.rectangle", box.rectangle)

    ### Make Box Plot Outliers Circles
    outlier.color <- "black"
    plot.symbol <- trellis.par.get("plot.symbol")
    plot.symbol$col <- outlier.color
    plot.symbol$cex <- 1
    trellis.par.set("plot.symbol", plot.symbol)

    ### Make Box Plot Whiskers Black, Solid, and See Through
    whisker.color <- "black"
    box.umbrella <- trellis.par.get("box.umbrella")
    box.umbrella$alpha <- ci95.ghost
    box.umbrella$col <- whisker.color
    box.umbrella$lty <- "solid"
    trellis.par.set("box.umbrella", box.umbrella)

    ### Make Whiskers and Outliers
    if(whiskers.and.outliers){
      panel.bwplot(
        x = rep(x,length(y)),
        y = y,
        horizontal = FALSE,
        color = "white",  ### Best way known how to remove the dot
        pch=".", ### Best way known how to remove the dot
        cex = 0.000001, ### Best way known how to remove the dot
        fill = "transparent",  # Makes box see-through
        box.width = 0 # Makes whisker top line disappear
      )
    }




#cat("\n\n\nX");print(x)
#cat("a");print(a)
#cat("s");print(s)
#cat("n");print(n)
#cat("error");print(error)
#cat("top.ci");print(top.ci)
#cat("bot.ci");print(bot.ci)
#cat("diff");print(0.02*diff(y.limits))

  }
  
}

Legend Info

key = list(
  title = "Legend",
  text = list(
    c("Points"),
    col="black"
  ),
  points = list(
    col = c("black"),
    pch = c(4),
    cex = c(1)*0.75
  ),
  lines = list(
    col = c("black"),
    lwd = c(1)*0.75,
    lty = c("blank")
  ),
  type = "l",
  space = "right",
  cex.title = 1,
  cex = 0.75
)