plot.factorplot {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 class '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
)

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

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).

Author(s)

Dave Armstrong

See Also

factorplot

Examples

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)