SAFE plot
Description
A SAFE plot for a given category displays the empirical distribution function for the ranked (or unranked) local statistics of a given category.
Usage
1 2 3 4 5 
Arguments
safe 
Object of class 
cat.name 
Name of the category to be plotted. If omitted, the most significant category is plotted. 
limits 
Limits of the shaded region in the plot on the unranked scale 
c.vec 
Logical vector specifying membership to a gene category 
local.stats 
Numeric vector of local statistics 
gene.names 
Optional character vector to replace

rank 
Logical to plotted raned (TRUE) or unranked (FALSE) local statistics on the xaxis 
x.limits 
Optional limits of the xaxis. By default will be range(local.stats) 
c.thresh 
Optional threshold for plotting tickmarks for a weighted (“soft”) gene category 
colors 
Optional vector specificy colors for gene labels 
x.ticks 
Optional location of xaxis tick marks on the ranked scale 
t.cex 
Text size for gene labels 
p.val 
Optional numeric value of the category's empirical pvalue 
cat.desc 
Optional character string as a subtitle beneath the category name 
title 
Optional title to the plot 
... 
Allows arguments from version 2.0 to be ignored 
Details
SAFEplots display the differential expression in a given category relative to the complementary set of genes. The empirical cumulative distribution is plotted for local statistics in the category, on either a ranked or unranked scale. Tick marks are drawn along the top of the graph to indicate each gene's positions, and labeled when sufficient space permits. In this manner, genes with the most extreme local statistics can be identified as contributing to the category's significance.
Typical usages are
1 2 3  safeplot(safe)
safeplot(safe, cat.name)
safeplot(c.vec, local.stats, p.val, limits)

Author(s)
William T. Barry: bbarry@jimmy.harvard.edu
References
W. T. Barry, A. B. Nobel and F.A. Wright, 2005, Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics 21(9) 1943–1949.
See also the vignette included with this package.
See Also
safe
.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31  ## Simulate a dataset with 1000 genes and 20 arrays in a 2sample design.
## The top 100 genes will be differentially expressed at varying levels
g.alt < 100
g.null < 900
n < 20
data<matrix(rnorm(n*(g.alt+g.null)),g.alt+g.null,n)
data[1:g.alt,1:(n/2)] < data[1:g.alt,1:(n/2)] +
seq(2,2/g.alt,length=g.alt)
dimnames(data) < list(c(paste("Alt",1:g.alt),
paste("Null",1:g.null)),
paste("Array",1:n))
## A treatment vector
trt < rep(c("Trt","Ctr"),each=n/2)
## 2 alt. categories and 18 null categories of size 50
C.matrix < kronecker(diag(20),rep(1,50))
dimnames(C.matrix) < list(dimnames(data)[[1]],
c(paste("TrueCat",1:2),paste("NullCat",1:18)))
dim(C.matrix)
results < safe(data,trt,C.mat = C.matrix,Pi.mat = 100)
results
## SAFEplot made for the first category
if (interactive()) {
safeplot(results,"TrueCat 1")
}

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