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#' Test for colors in classes distribution for folders
#'
#' @param path path to folder
#' @param test "Wilcoxon", "wilcox" or "U" for Wilcoxon rank-sum (Mann-Whitney U), chisq for Chi-squared test
#'
#' @return test results
#' @export
#' @import stats
#'
t_colors.in.classes.folder<-function(path,test="Wilcoxon")
{
orig<-getwd()
setwd(path)
cic<-loadcic()*100
if (test=="chisq"){
cic<-apply(cic,1:2,sum)
cat("Chi-squared test\n
DAPI vs. color 1, p-value ")
ch1<-nucim.chisq.test(cic[,1],cic[,2])
nucim.print.p(ch1$p.value,8)
cat("\n")
if (dim(cic)[2]==3)
{
cat("DAPI vs. color 2, p-value ")
ch2<-nucim.chisq.test(cic[,1],cic[,3])
nucim.print.p(ch2$p.value,8)
cat("\n")
cat("color1 vs. color 2, p-value = ")
ch3<-nucim.chisq.test(cic[,2],cic[,3])
nucim.print.p(ch3$p.value,8)
cat("\n")
}
}
if (test=="wilcox"|test=="Wilcoxon"|test=="U"){
cic <- round(cic)
N <- dim(cic)[1]
l <- dim(cic)[2]
f <- dim(cic)[3]
cic2 <- vector(length=l,mode="list")
for (j in 1:l){
for (i in 1:f){
cic2[[j]]<-c(cic2[[j]],rep(1:N,cic[,j,i]))
}
}
cat("Wilcoxon Rank Sum test\n
DAPI vs. color 1, p-value ")
ch1=wilcox.test(cic2[[1]],cic2[[2]])
nucim.print.p(ch1$p.value,8)
cat("\n")
if (dim(cic)[2]==3)
{
cat("DAPI vs. color 2, p-value ")
ch2=wilcox.test(cic2[[1]],cic2[[3]])
nucim.print.p(ch2$p.value,8)
cat("\n")
cat("color1 vs. color 2, p-value ")
ch3=wilcox.test(cic2[[2]],cic2[[3]])
nucim.print.p(ch3$p.value,8)
cat("\n")
}
}
setwd(orig)
}
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