plot.freqMAP: Plotting Frequency Moving Average Plot (MAP) Objects

In freqMAP: Frequency Moving Average Plots (MAP) of Multinomial Data by a Continuous Covariate

Description

This function can plot a single frequency MAP object, can overlay two frequency MAP object plots, and can plot odds ratios (OR) comparing two frequency MAP objects.

Usage

## S3 method for class 'freqMAP'
plot(x, y = NULL, xlim = NULL, ylim = NULL,
              legend = NULL,
              show.p.value.legend = FALSE,
              type = "freq", 
	      p.value.bar.alpha = c(0.05, 0.01),
    	      p.value.bar.color=c("gray90","darkgray"),
              cex=1,cex.axis=1,cex.lab=1,cex.main=1,
              pch.x=2,lty.x=1,lwd.x=1,col.x="red",
              pch.y=1,lty.y=2,lwd.y=1,col.y="blue",
              cex.legend=1,
              layout.matrix = NULL,...)

Arguments

x	A freqMAP object, usually the result of a call to freqMAP
y	An optional freqMAP object, usually the result of a call to freqMAP
xlim	Limits on the x-axis. Must be a vector of length 2. The same limits will be used for all category or OR plots. If not specified, then the function will calculate reasonable limits.
ylim	Limits on the y-axis. If type="freq", then ylim must be a matrix with 2 columns and as many rows as the length of x$cat.names. In this case, row i will be used as the y limits on the frequency plot of category i. If type="or", then ylim must be a vector of length 2 specifying the common y limits for all odds ratio plots. If ylim is not specified, then the function will calculate reasonable limits which will be common on all plots.
legend	A 2-vector of strings specifying legend text for the x and y freqMAP objects when type="freq". This argument is ignored when type="or" or if y is not specified.
show.p.value.legend	When set to TRUE, a legend is generated for the two levels of Bayesian p-values plotted. This argument is ignored when y is not specified.
type	The type of plot to generate. Must be either "freq" or "or". See Details below.
p.value.bar.alpha	A 2-vector of p-value cutoffs for the p-value bar at the bottom of plots. This argument is ignored if y is not specified. See Details below.
p.value.bar.color	A 2-vector of strings specifying the shading colors for the p-value bar at the bottom of plots. This argument is ignored if y is not specified. See Details below.
cex	The size of plotting characters.
cex.axis	The value passed to cex.axis in all plots. See ?par for details.
cex.lab	The value passed to cex.lab in all plots. See ?par for details.
cex.main	The value passed to cex.main in all plots. See ?par for details.
pch.x	The plotting character used for the freqMAP object in x.
lty.x	The line type lty for the posterior bounds in the freqMAP object in x.
lwd.x	The line width lwd for the posterior bounds in the freqMAP object in x.
col.x	The plotting color for the freqMAP object in x.
pch.y	The plotting character used for the freqMAP object in y.
lty.y	The line type lty for the posterior bounds in the freqMAP object in y.
lwd.y	The line width lwd for the posterior bounds in the freqMAP object in y.
col.y	The plotting color for the freqMAP object in y.
cex.legend	The cex parameter passed to all legends. See ?legend for details.
layout.matrix	The matrix passed to layout() prior to plotting. When this argument is not used, the default behavior is to show all plots on the same figure stacked vertically.
...	Not used at this time.

Details

Three types of plots are possible. First, if y is not specified, then a frequency MAP will be plotted for each category in the x object. The mean is plotted surrounded by 95% central posterior intervals (CPI). Second, if y is specified and type="freq", then a frequency MAP will be plotted for each category in the x and y objects, where the two frequency MAPs are overlaid on each category plot. Third, if y is specified and type="or", then a plot is made for all odds ratios comparing each pair of categories. The posterior mean OR and 95% CPI on the OR are plotted. The title of each OR plot gives the direction of the OR. For example, if there are two categories "a" and "b", and the plot title says "b" vs. "a", this indicates the OR plotted is (t\_xb t\_ya) / (t\_xa t\_yb), where t\_xj and t\_yj indicate the true frequency of category j in the x and y MAPs, respectively. If type="or", plotting characters, line types, line widths, and colors are controlled by pch.x, lty.x, lwd,x, and col.x.

If y is specified, then x and y must have the same values in their elements [["cat.names"]], [["cat.short"]], and [["hw"]]. The [["x.label"]] element can be different. (This element indicates the name of the column in the [["cat.ma"]] element which contains the x values when plotting.)

When y is specified, a gray bar is added to the bottom of the plot when the two frequency plots are "significantly" different. When type="freq", significance is defined as the posterior Pr(category frequency in MAP x > category frequency in MAP y) > alpha/2 or < (1-alpha/2). When type="or", significance is defined as the posterior Pr( OR(category 1 vs. category 2) > 1 ) > alpha/2 or < (1-alpha/2). The value of alpha is defined at two levels by the p.value.bar.alpha argument and plotted in light gray (higher alpha) and dark gray (lower alpha). The shading colors of the two alpha levels can be overridden by the p.value.bar.color argument. This can be thought of as a Bayesian analog to a two-sided p-value. See posterior.comparison.freqMAP for further details.

Specifying a legend or asking for a p-value legend, while not specifying xlim, will cause the x axis limits to be expanded 20% on the left side to give room for the legend.

Along with the example given below, see freqMAP-package for an example based on genotype data.

Author(s)

Colin McCulloch <[e-mail]>

References

Payami, H., Kay, D.M., Zabetian, C.P., Schellenberg, G.D., Factor, S.A., and McCulloch, C.C. (2009) "Visualizing Disease Associations: Graphic Analysis of Frequency Distributions as a Function of Age Using Moving Average Plots (MAP) with Application to Alzheimer's and Parkinson's Disease", Genetic Epidemiology

See Also

freqMAP, summary.freqMAP, layout

Examples

  #Make two sets of 2-category frequency data, y1 & y2, which both vary as
  #a function of a continuous variable x
  set.seed(5)
  x <- runif(2000,min=-2,max=2)
  y1 <- c("a","b")[1+rbinom(n=length(x),size=rep(1,length(x)),prob=pnorm(x/2))]
  y2 <- c("a","b")[1+rbinom(n=length(x),size=rep(1,length(x)),prob=pnorm(x/5))]

  #Create the frequency MAP objects for y1 and y2
  fp1 <- freqMAP(data.frame(x=x,y=y1,stringsAsFactors=FALSE),
                  x=seq(-2,2,by=.2),x.label="x",hw=.2)
  fp2 <- freqMAP(data.frame(x=x,y=y2,stringsAsFactors=FALSE),
                  x=seq(-2,2,by=.2),x.label="x",hw=.2)

  #Examine the frequency MAP objects
  summary(fp1)
  print(fp2)

  #Compare the posterior distributions on the two frequency MAPs
  pc <-  posterior.comparison.freqMAP(group1=fp1,group2=fp2)

  #Three example plots
  plot(fp1,ylim=matrix(c(0,1),nrow=2,ncol=2,byrow=TRUE))
  plot(fp1,fp2,type="freq",legend=c("y1","y2"),show.p.value.legend=TRUE)
  plot(fp1,fp2,type="freq",legend=c("y1","y2"),show.p.value.legend=TRUE,
       p.value.bar.color=c("green","yellow"))
  
  plot(fp1,fp2,type="or")

freqMAP documentation built on May 29, 2017, 11:42 p.m.