plot.factorplot: Plot method for objects of class factorplot

Description

Creates a plot akin to an upper-triangular levelplot (though using plot rather than levelplot) where the coloring of the squares represents significance and text inside the squares represents the pairwise difference and its correspopnding standard error.

Usage

# S3 method for factorplot
plot(
  x,
  ...,
  abbrev.char = 10,
  polycol = NULL,
  textcol = NULL,
  trans = NULL,
  print.sig.leg = TRUE,
  print.square.leg = TRUE,
  scale.text = 1,
  space.text = 1,
  print.est = TRUE,
  print.se = TRUE
)

Value

a graph: For m categories, the plot returns an m-1 x m-1 matrix where the nexus of the row and column values represent the pairwise differencee between the row and column values along with the standard error of the difference on the linear scale (unless a transformation is performed).

Arguments

x: An object of class factorplot, produced by factorplot.
...: Other arguments to be passed to plot, currently not implemented
abbrev.char: The number of characters that should be used to abbreviate the levels of the factor. Set to a large value for unabbreviated names.
polycol: A vector of three colors indicating the colors of polygons when the difference is significant negative, insignificant, and significant positive, in that order. Defaults to c(‘gray80’, ‘white’, ‘gray40’).
textcol: A vector of three colors indicating the text color for polygons that are significant negative, insignificant, and significant positive, in that order. Defaults to c(‘black’, ‘black’, ‘white’)
trans: A character string representing the post-hypothesis-testing transformation to be performed on the estimates. For example, if the estimates provided to the factorplot command are log-floating absolute risks, you could use the transformation ‘exp’. The transformation is performed through a call to do.call
print.sig.leg: logical indicating whether the legend identifying the meaning of the different colors should be included.
print.square.leg: logical indicating whether the legend identifying the meaning of the numbers in each square should be included.
scale.text: optional scale factor to be applied to text, numbers bigger than 1 make text bigger than default and numbers smaller than 1 do the opposite
space.text: optional text spacing factor, numbers bigger than 1 push text toward the extent of the boxes and numbers smaller than one bring text in toward the center
print.est: logical argument indicating whether the estimates should be printed in the boxes
print.se: logical argument indicating whether the standard errors should be printed in the boxes

Author

Dave Armstrong

Examples

Run this code


est1 <- log(c(1.00,2.12,1.44,1.31,1.44,
     1.46,0.90))
var1 <- c(0.242,0.096,0.156,0.140,
     0.380,0.484,0.375)^2
names(est1) <- c(
     "Normal & superficial gastritis", 
     "Chronic gastritis", 
     "Chronic atrophic gastritits", 
     "Intestinal metaplasia I", 
     "Intestinal metaplasia II", 
     "Intestinal metaplasia III", 
     "Dysplasia")

plummer_fp1 <- factorplot(est1, var=var1, resdf=Inf)
plot(plummer_fp1, trans="exp", abbrev.char = 100)