plot.DiscreteFDR {DiscreteFDR} R Documentation

## 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(1, 1, 1),
lwd = c(1, 1, 1),
type.crit = "b",
legend = NULL,
...
)


### Arguments

 x an object of class "DiscreteFDR". col a numeric or character vector of length 3 indicating the colors of the rejected p-values accepted p-values critical values (if present). pch a numeric or character vector of length 3 indicating the point characters of the rejected p-values accepted p-values critical values (if present and type.crit is a plot type like 'p', 'b' etc.). lwd a numeric vector of length 3 indicating the thickness of the points and lines. 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

#Construction of the p-values and their support
df.formatted <- fisher.pvalues.support(counts = df, input = "noassoc")
raw.pvalues <- df.formatted$raw pCDFlist <- df.formatted$support

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



[Package DiscreteFDR version 1.3.6 Index]