plot.DiscreteFDR {DiscreteFDR}

Plot Method for DiscreteFDR objects

Description

Plots raw p-values of a DiscreteFDR object and highlights rejected and accepted p-values. If present, the critical values are plotted, too.

Usage

## S3 method for class 'DiscreteFDR'
plot(
  x,
  col = c(2, 4, 1),
  pch = c(20, 20, 17),
  lwd = rep(par()$lwd, 3),
  cex = rep(par()$cex, 3),
  type.crit = "b",
  legend = NULL,
  ...
)

Arguments

x

object of class DiscreteFDR.

col

numeric or character vector of length 3 indicating the colors of the

1. rejected p-values

2. accepted p-values

3. critical values (if present).

pch

numeric or character vector of length 3 indicating the point characters of the

1. rejected p-values

2. accepted p-values

3. critical values (if present and type.crit is a plot type like 'p', 'b' etc.).

lwd

numeric vector of length 3 indicating the thickness of the points and lines; defaults to current par()$lwd setting.

cex

numeric vector of length 3 indicating the size of point characters or lines of the

1. rejected p-values

2. accepted p-values

3. critical values (if present).

defaults to current par()$cex setting.

type.crit

1-character string giving the type of plot desired for the critical values (e.g.: 'p', 'l' etc; see plot()).

legend

if NULL, no legend is plotted; otherwise expecting a character string like "topleft" etc. or a numeric vector of two elements indicating (x, y) coordinates.

...

further arguments to plot.default().

Examples

X1 <- c(4, 2, 2, 14, 6, 9, 4, 0, 1)
X2 <- c(0, 0, 1, 3, 2, 1, 2, 2, 2)
N1 <- rep(148, 9)
N2 <- rep(132, 9)
Y1 <- N1 - X1
Y2 <- N2 - X2
df <- data.frame(X1, Y1, X2, Y2)
df

# Compute p-values and their supports of Fisher's exact test
test.result <- generate.pvalues(df, "fisher")
raw.pvalues <- test.result$get_pvalues()
pCDFlist <- test.result$get_pvalue_supports()

DBH.su.fast <- DBH(raw.pvalues, pCDFlist)
DBH.su.crit <- DBH(raw.pvalues, pCDFlist, ret.crit.consts = TRUE)
DBH.sd.fast <- DBH(test.result, direction = "sd")
DBH.sd.crit <- DBH(test.result, direction = "sd", ret.crit.consts = TRUE)

plot(DBH.sd.fast)
plot(DBH.sd.crit, xlim = c(1, 5), ylim = c(0, 0.4))
plot(DBH.su.fast, col = c(2, 4), pch = c(2, 3), lwd = c(2, 2), 
     legend = "topleft", xlim = c(1, 5), ylim = c(0, 0.4))
plot(DBH.su.crit, col = c(2, 4, 1), pch = c(1, 1, 4), lwd = c(1, 1, 2), 
     type.crit = 'o', legend = c(1, 0.4), lty = 1, xlim = c(1, 5), 
     ylim = c(0, 0.4))