source("bioxm.R")

library(multtest)
library(lattice)
library(scatterplot3d)


sink()
t <- as.matrix(getDataInReport());

t1 <- t[,(2:3)]


X <- t(sapply(1:nrow(t1), function(r) c(as.numeric(unlist(strsplit(t1[r,], ';'))))))
rownames(X) <- t[,1]

num.group1 <- length(unlist(strsplit(t1[1,1],';')))
num.group2 <- length(unlist(strsplit(t1[1,2],';')))
cl <- c(rep(0, num.group1), rep(1, num.group2))

means.group1 = apply(X[,1:num.group1], 1, mean)
means.group2 = apply(X[,(num.group1+1):(num.group1+num.group2)], 1, mean)

means.group1 = round(means.group1, digits=2)
means.group2 = round(means.group2, digits=2)

resT <- mt.maxT(X, classlabel=cl, B=200)
ord <- order(resT$index)
adjp.BH <- mt.rawp2adjp(rawp=resT$rawp[ord], proc=c("BH"))

stat <- round(resT$teststat, digits=2)
res <- cbind(means.group1[ord], means.group2[ord], stat, resT$rawp, adjp.BH$adjp[ord, "BH"])

colnames(res) <- c("means.group1", "means.group2", "statistic", "rawp", "adjp.BH")

res <- res[names(sort(res[,'adjp.BH'], decreasing=FALSE)), ]
write.table(res, sep="\t", quote=FALSE, file=outfile)

labels <- rownames(res[1:3,])
labels <- strsplit(labels, ":")
xlab <- labels[[1]][3]
ylab <- labels[[2]][3]
zlab <- labels[[3]][3]
scatterplot3d(t(X[rownames(res[1:3,]),]), 
              xlab=xlab, ylab=ylab, zlab=zlab, 
              color=c(rep("darkgreen", num.group1), rep("red", num.group2)), 
              font.lab=2, cex.lab=0.6, cex.axis = 0.6, cex=0.8, pch=21, type='h' ) 
#color<-c(rep("green", num.group1), rep("red", num.group2))