plot.DiscreteFWER {DiscreteFWER} | R Documentation |
Plot Method for DiscreteFWER
objects
Description
Plots raw p-values of a DiscreteFWER
object and highlights rejected and
accepted p-values. If calculated, the critical values are plotted, too.
Usage
## S3 method for class 'DiscreteFWER'
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 |
col |
numeric or character vector of length 3 indicating the colours of the
|
pch |
numeric or character vector of length 3 indicating the point characters of the
|
lwd |
numeric vector of length 3 indicating the thickness of the
points and lines; defaults to current |
cex |
numeric vector of length 3 indicating the size of point characters or lines of the
defaults to current |
type_crit |
1-character string giving the type of plot desired for the
critical values (e.g.: |
legend |
if |
... |
further arguments to |
Value
A plot is created, but no value is returned.
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
# Computation of p-values and their supports with Fisher's exact test
library(DiscreteTests) # for Fisher's exact test
test_results <- fisher_test_pv(df)
raw_pvalues <- test_results$get_pvalues()
pCDFlist <- test_results$get_pvalue_supports()
DBonf_fast <- DBonferroni(raw_pvalues, pCDFlist)
DBonf_crit <- DBonferroni(test_results, critical_values = TRUE)
DHolm_fast <- DHolm(test_results)
DHolm_crit <- DHolm(raw_pvalues, pCDFlist, critical_values = TRUE)
plot(DBonf_fast)
plot(DBonf_crit, xlim = c(1, 5), ylim = c(0, 0.4))
plot(DHolm_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(DHolm_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))