otplot: Plot a factor variable by discrete categories

In tobyjohnson/gtx: Genetics ToolboX

Description

Plots a factor variable (such as binary yes/no, case/control, or an ordinal trait) by discrete categories (such as genotype).

Usage

## S3 method for class 'character'
otplot(object, x, data, ylab, xlab, col, col.mix = c("white", "black"), style = "percent", ycrop = FALSE, yext = 1.25)
## S3 method for class 'factor'
otplot(object, x, data, ylab, xlab, col, col.mix = c("white", "black"), style = "percent", ycrop = FALSE, yext = 1.25)
## S3 method for class 'numeric'
otplot(object, x, data, ylab, xlab, col, col.mix = c("white", "black"), style = "percent", ycrop = FALSE, yext = 1.25)

Arguments

object	The name or values of the factor variable
x	The name or values of the discrete category variable
data	A data frame containing values
ylab	A label for the y axis
xlab	A label for the x axis
col	A vector of colours for levels of x
col.mix	A pair of colours to mix with col for levels of object
style	A character vector, see details
ycrop	Logical, whether to crop y axis to data range
yext	Extension of y axis to accomodate legend

Details

Generates a plot displaying factor data by levels of a factor.

Currently, all supported styles are variations on a barplot, with bar heights showing either the count, fraction, or percentage of the response factor object.

Colour mixing is not currently as flexible as it could be.

Legend placement heuristics could be improved.

Value

Returns an invisible null. The plot is generated as a side effect.

Author(s)

Toby Johnson [e-mail]

Examples

  data(aoex1)
  aoex1 <- within(aoex1, {
                  bmicat <- cut(aoex1$bmi, 
                                c(-Inf, 25, 30, Inf))})
  ## Simple example
  with(aoex1, otplot(bmicat, rs123456, 
         ylab = "BMI category", xlab = "rs123456 genotype"))
  ## Illustration of different plot styles,
  ## using alternative function calling style
  oldpar <- par(mfcol = c(2, 3))
  for (style1 in c("percent", "percentall", "fraction", "fractionall", "count")) {
    otplot("bmicat", "rs123456", aoex1,
           ylab = "BMI category", xlab = "rs123456 genotype",
           style = style1)
    title(main = paste('style = "', style1, '"', sep = ""))
  }
  par(oldpar)
  ## Numerics are coerced to factors
  with(aoex1, otplot(rs123456_A, rs123456, 
         ylab = "Numeric genotype", xlab = "rs123456 genotype"))
  ## Illustration of alternative colour scheme      
  otplot("bmicat", "rs123456", aoex1,
         ylab = "BMI category", xlab = "rs123456 genotype",
         col = rgb(.3, 0, .15),
         col.mix = c(rgb(1, 1, .9), rgb(0, 0, .4)))

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.