File:Scatterhist.svg

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Original file(SVG file, nominally 563 × 563 pixels, file size: 70 KB)

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"))

File history

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Date/TimeThumbnailDimensionsUserComment
current13:33, 1 October 2018Thumbnail for version as of 13:33, 1 October 2018563 × 563 (70 KB)Brb (talk | contribs)The R source code is at https://gist.github.com/arraytools/7005670b9d4b34e45f45131a6f87d8f4#file-scatterhist_null
13:21, 1 October 2018Thumbnail for version as of 13:21, 1 October 2018563 × 563 (70 KB)Brb (talk | contribs)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...

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