File:Scatterhist.svg - Revision history

Brb at 14:22, 16 February 2024

2024-02-16T14:22:04Z

← Older revision		Revision as of 10:22, 16 February 2024
Line 1:		Line 1:
			<syntaxhighlight lang='r'>
	scatterhist <- function(x, y, xlab="", ylab=""){		scatterhist <- function(x, y, xlab="", ylab=""){
	zones=matrix(c(2,0,1,3), ncol=2, byrow=TRUE)		zones=matrix(c(2,0,1,3), ncol=2, byrow=TRUE)
Line 32:		Line 33:
	t3 <- topTable(fit3,coef=1, number = Inf)		t3 <- topTable(fit3,coef=1, number = Inf)
	with(t3, scatterhist(P.Value, adj.P.Val, xlab = "P-value", ylab = "BH adjusted P"))		with(t3, scatterhist(P.Value, adj.P.Val, xlab = "P-value", ylab = "BH adjusted P"))
			</syntaxhighlight>

Brb: Brb uploaded a new version of File:Scatterhist.svg

2018-10-01T17:33:18Z

Brb uploaded a new version of File:Scatterhist.svg

← Older revision		Revision as of 13:33, 1 October 2018
(No difference)

Brb: scatterhist <- function(x, y, xlab="", ylab=""){ zones=matrix(c(2,0,1,3), ncol=2, byrow=TRUE) layout(zones, widths=c(4/5,1/5), heights=c(1/5,4/5)) xhist = hist(x, plot=FALSE) yhist = hist(y, plot=FALSE) top = max(c(xhist$counts, yhi...

2018-10-01T17:21:41Z

New page

scatterhist <- function(x, y, xlab="", ylab=""){
zones=matrix(c(2,0,1,3), ncol=2, byrow=TRUE)
layout(zones, widths=c(4/5,1/5), heights=c(1/5,4/5))
xhist = hist(x, plot=FALSE)
yhist = hist(y, plot=FALSE)
top = max(c(xhist$counts, yhist$counts))
par(mar=c(3,3,1,1))
plot(x,y)
par(mar=c(0,3,1,1))
barplot(xhist$counts, axes=FALSE, ylim=c(0, top), space=0)
par(mar=c(3,0,1,1))
barplot(yhist$counts, axes=FALSE, xlim=c(0, top), space=0, horiz=TRUE)
par(oma=c(3,3,0,0))
mtext(xlab, side=1, line=1, outer=TRUE, adj=0,
at=.4)
mtext(ylab, side=2, line=1, outer=TRUE, adj=0,
at=.4)
}

library(limma)
set.seed(1234)
n <- 100
testexpr <- matrix(rnorm(n * 10, 5, 1), nc= 10)

design3 <- model.matrix(~ 0 + as.factor(c(rep(1,5), rep(2, 5))))
colnames(design3) <- c("A", "B")

fit3 <- lmFit(testexpr,design3)
contrasts.matrix3 <- makeContrasts("AvsB"=A-B, levels = design3)
fit3 <- eBayes(contrasts.fit(fit3, contrasts=contrasts.matrix3))

t3 <- topTable(fit3,coef=1, number = Inf)
with(t3, scatterhist(P.Value, adj.P.Val, xlab = "P-value", ylab = "BH adjusted P"))