#' @title Perform the Reverse Hourglass Test
#' @description The \emph{Reverse Hourglass Test} aims to statistically evaluate the
#' existence of a reverse hourglass pattern based on \code{\link{TAI}} or \code{\link{TDI}} computations.
#' The corresponding p-value quantifies the probability that a given TAI or TDI pattern (or any phylotranscriptomics pattern)
#' does follow an hourglass like shape. A p-value < 0.05 indicates that the corresponding phylotranscriptomics pattern does
#' rather follow a reverse hourglass (low-high-low) shape.
#' @param ExpressionSet a standard PhyloExpressionSet or DivergenceExpressionSet object.
#' @param modules a list storing three elements: early, mid, and late. Each element expects a numeric
#' vector specifying the developmental stages or experiments that correspond to each module.
#' For example, \code{module} = list(early = 1:2, mid = 3:5, late = 6:7) devides a dataset
#' storing seven developmental stages into 3 modules.
#' @param permutations a numeric value specifying the number of permutations to be performed for the \code{ReverseHourglassTest}.
#' @param lillie.test a boolean value specifying whether the Lilliefors Kolmogorov-Smirnov Test shall be performed to quantify the goodness of fit.
#' @param plotHistogram a boolean value specifying whether a \emph{Lillifor's Kolmogorov-Smirnov-Test}
#' shall be performed to test the goodness of fit of the approximated distribution, as well as additional plots quantifying the significance
#' of the observed phylotranscriptomic pattern.
#' @param runs specify the number of runs to be performed for goodness of fit computations, in case \code{plotHistogram} = \code{TRUE}.
#' In most cases \code{runs} = 100 is a reasonable choice. Default is \code{runs} = 10 (because it takes less computation time for demonstration purposes).
#' @param parallel performing \code{runs} in parallel (takes all cores of your multicore machine).
#' @param gof.warning a logical value indicating whether non significant goodness of fit results should be printed as warning. Default is \code{gof.warning = FALSE}.
#' @param custom.perm.matrix a custom \code{\link{bootMatrix}} (permutation matrix) to perform the underlying test statistic. Default is \code{custom.perm.matrix = NULL}.
#' @details
#' The reverse hourglass test is a permutation test based on the following test statistic.
#'
#' (1) A set of developmental stages is partitioned into three modules - early, mid, and late - based on prior biological knowledge.
#'
#' (2) The mean \code{\link{TAI}} or \code{\link{TDI}} value for each of the three modules T_early, T_mid, and T_late are computed.
#'
#' (3) The two differences \code{D1 = T_mid - T_early} and \code{D2 = T_mid - T_late} are calculated.
#'
#' (4) The minimum \code{D_min} of \code{D1} and \code{D2} is computed as final test statistic of the reductive hourglass test.
#'
#'
#' In order to determine the statistical significance of an observed minimum difference D_min
#' the following permutation test was performed. Based on the \code{\link{bootMatrix}} D_min
#' is calculated from each of the permuted \code{\link{TAI}} or \code{\link{TDI}} profiles,
#' approximated by a Gaussian distribution with method of moments estimated parameters returned by \code{\link[fitdistrplus]{fitdist}},
#' and the corresponding p-value is computed by \code{\link{pnorm}} given the estimated parameters of the Gaussian distribution.
#' The \emph{goodness of fit} for the random vector \emph{D_min} is statistically quantified by an Lilliefors (Kolmogorov-Smirnov) test for normality.
#'
#'
#' In case the parameter \emph{plotHistogram = TRUE}, a multi-plot is generated showing:
#'
#' (1) A Cullen and Frey skewness-kurtosis plot generated by \code{\link[fitdistrplus]{descdist}}.
#' This plot illustrates which distributions seem plausible to fit the resulting permutation vector D_min.
#' In the case of the \emph{Reverse Hourglass Test} a normal distribution seemed plausible.
#'
#' (2) A histogram of \code{D_min} combined with the density plot is plotted. D_min is then fitted by a normal distribution.
#' The corresponding parameters are estimated by \emph{moment matching estimation} using the \code{\link[fitdistrplus]{fitdist}} function.
#'
#' (3) A plot showing the p-values for N independent runs to verify that a specific p-value is biased by a specific permutation order.
#'
#' (4) A barplot showing the number of cases in which the underlying goodness of fit (returned by Lilliefors (Kolmogorov-Smirnov) test
#' for normality) has shown to be significant (\code{TRUE}) or not significant (\code{FALSE}).
#' This allows to quantify the permutation bias and their implications on the goodness of fit.
#' @return a list object containing the list elements:
#'
#' \code{p.value} : the p-value quantifying the statistical significance (low-high-low pattern) of the given phylotranscriptomics pattern.
#'
#' \code{std.dev} : the standard deviation of the N sampled phylotranscriptomics patterns for each developmental stage S.
#'
#' \code{lillie.test} : a boolean value specifying whether the \emph{Lillifors KS-Test} returned a p-value > 0.05,
#' which indicates that fitting the permuted scores with a normal distribution seems plausible.
#' @references
#'
#' Drost HG et al. (2015) Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012
#'
#' Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.
#'
#' M. L. Delignette-Muller, R. Pouillot, J.-B. Denis and C. Dutang (2014), fitdistrplus: help to fit
#' of a parametric distribution to non-censored or censored data.
#'
#' Cullen AC and Frey HC (1999) Probabilistic techniques in exposure assessment. Plenum Press, USA, pp. 81-159.
#'
#' Evans M, Hastings N and Peacock B (2000) Statistical distributions. John Wiley and Sons Inc.
#'
#' Sokal RR and Rohlf FJ (1995) Biometry. W.H. Freeman and Company, USA, pp. 111-115.
#'
#' Juergen Gross and bug fixes by Uwe Ligges (2012). nortest: Tests for Normality. R package version
#' 1.0-2.
#'
#' http://CRAN.R-project.org/package=nortest
#'
#' Dallal, G.E. and Wilkinson, L. (1986): An analytic approximation to the distribution of Lilliefors' test for normality. The American Statistician, 40, 294-296.
#'
#' Stephens, M.A. (1974): EDF statistics for goodness of fit and some comparisons. Journal of the American Statistical Association, 69, 730-737.
#'
#' http://stackoverflow.com/questions/4290081/fitting-data-to-distributions?rq=1
#'
#' http://stats.stackexchange.com/questions/45033/can-i-use-kolmogorov-smirnov-test-and-estimate-distribution-parameters
#'
#' http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf
#'
#' http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf
#'
#' @author Hajk-Georg Drost
#' @seealso \code{\link{reversehourglassScore}}, \code{\link{bootMatrix}}, \code{\link{FlatLineTest}}, \code{\link{EarlyConservationTest}}, \code{\link{PlotSignature}}
#' @examples
#'
#' data(PhyloExpressionSetExample)
#'
#' # perform the reductive hourglass test for a PhyloExpressionSet
#' # here the prior biological knowledge is that stages 1-2 correspond to module 1 = early,
#' # stages 3-5 to module 2 = mid (phylotypic module), and stages 6-7 correspond to
#' # module 3 = late
#' ReverseHourglassTest(PhyloExpressionSetExample,
#' modules = list(early = 1:2, mid = 3:5, late = 6:7),
#' permutations = 1000)
#'
#'
#' # use your own permutation matrix based on which p-values (ReverseHourglassTest)
#' # shall be computed
#' custom_perm_matrix <- bootMatrix(PhyloExpressionSetExample,100)
#'
#' ReverseHourglassTest(PhyloExpressionSetExample,
#' modules = list(early = 1:2, mid = 3:5, late = 6:7),
#' custom.perm.matrix = custom_perm_matrix)
#'
#'
#' @import foreach
#' @export
ReverseHourglassTest <- function(ExpressionSet,
modules = NULL,
permutations = 1000,
lillie.test = FALSE,
plotHistogram = FALSE,
runs = 10,
parallel = FALSE,
gof.warning = FALSE,
custom.perm.matrix = NULL)
{
is.ExpressionSet(ExpressionSet)
if (is.null(modules))
stop(
"Please specify the three modules: early, mid, and late using the argument 'modules = list(early = ..., mid = ..., late = ...)'.",
call. = FALSE
)
if (any(table(unlist(modules)) > 1))
stop("Intersecting modules are not defined for the ReductiveHourglassTest.",
call. = FALSE)
if (length(modules) != 3)
stop(
"Please specify three modules: early, mid, and late to perform the ReductiveHourglassTest.",
call. = FALSE
)
if (length(unlist(modules)) != (dim(ExpressionSet)[2] - 2))
stop(
"The number of stages classified into the three modules does not match the total number of stages stored in the given ExpressionSet.",
call. = FALSE
)
nCols <- dim(ExpressionSet)[2]
score_vector <-
vector(mode = "numeric", length = permutations)
resMatrix <- matrix(NA_real_, permutations, (nCols - 2))
real_age <- vector(mode = "numeric", length = nCols - 2)
real_age <-
cpp_TAI(as.matrix(dplyr::select(
ExpressionSet, 3:ncol(ExpressionSet)
)), as.vector(unlist(dplyr::select(
ExpressionSet, 1
))))
### compute the real reductive hourglass scores of the observed phylotranscriptomics pattern
real_score <- reversehourglassScore(
real_age,
early = modules[[1]],
mid = modules[[2]],
late = modules[[3]],
method = "min",
scoringMethod = "mean-mean",
profile.warn=T
)
options(warn=1)
### compute the bootstrap matrix
if (is.null(custom.perm.matrix)) {
resMatrix <-
cpp_bootMatrix(
as.matrix(dplyr::select(
ExpressionSet, 3:ncol(ExpressionSet)
)),
as.vector(unlist(
dplyr::select(ExpressionSet, 1)
)),
as.numeric(permutations)
)
}
else if (!is.null(custom.perm.matrix)) {
resMatrix <- custom.perm.matrix
}
### compute the global phylotranscriptomics destruction scores foe each sampled age vector
score_vector <-
apply(
resMatrix,
1 ,
reversehourglassScore,
early = modules[[1]],
mid = modules[[2]],
late = modules[[3]],
method = "min",
scoringMethod = "mean-mean"
)
# parameter estimators using MASS::fitdistr
param <-
fitdistrplus::fitdist(score_vector, "norm", method = "mme")
mu <- param$estimate[1]
sigma <- param$estimate[2]
if (plotHistogram == TRUE) {
# plot histogram of scores
normDensity <- function(x) {
return(stats::dnorm(x, mu, sigma))
}
if (lillie.test)
graphics::par(mfrow = c(2, 2))
if (!lillie.test)
graphics::par(mfrow = c(1, 3))
fitdistrplus::descdist(score_vector, boot = permutations)
graphics::curve(
expr = normDensity,
xlim = c(
min(score_vector, real_score),
max(score_vector, real_score)
),
col = "steelblue",
lwd = 5,
xlab = "Scores",
ylab = "Frequency"
)
graphics::hist(
x = score_vector,
prob = TRUE,
add = TRUE,
breaks = permutations / (0.01 * permutations)
)
graphics::rug(score_vector)
# plot a red line at the position where we can find the real rh value
graphics::abline(v = real_score,
lwd = 5,
col = "darkred")
p.vals_vec <-
vector(mode = "numeric", length = runs)
lillie_vec <-
vector(mode = "logical", length = runs)
rht <- vector(mode = "list", length = 3)
cat("\n")
if (parallel) {
### Parallellizing the sampling process using the 'doParallel' and 'parallel' package
### register all given cores for parallelization
par_cores <-
parallel::makeForkCluster(parallel::detectCores())
doParallel::registerDoParallel(par_cores)
# perform the sampling process in parallel
parallel_results <-
foreach::foreach(
i = 1:runs,
.combine = "rbind",
.errorhandling = "stop"
) %dopar% {
data.frame(
ReverseHourglassTest(
ExpressionSet = ExpressionSet,
permutations = permutations,
lillie.test = TRUE,
plotHistogram = FALSE,
modules = modules
)[c(1, 3)]
)
}
parallel::stopCluster(par_cores)
colnames(parallel_results) <-
c("p.value", "lillie.test")
p.vals_vec <- parallel_results[ , "p.value"]
lillie_vec <-
parallel_results[ , "lillie.test"]
}
if (!parallel) {
# sequential computations of p-values
# if(runs >= 10){
# # initializing the progress bar
# progressBar <- txtProgressBar(min = 1,max = runs,style = 3)
#
# }
for (i in 1:runs) {
if (lillie.test) {
rht <- ReverseHourglassTest(
ExpressionSet = ExpressionSet,
permutations = permutations,
lillie.test = TRUE,
plotHistogram = FALSE,
modules = list(
early = modules[[1]],
mid = modules[[2]],
late = modules[[3]]
),
runs = NULL
)
}
if (!lillie.test) {
rht <- ReverseHourglassTest(
ExpressionSet = ExpressionSet,
permutations = permutations,
lillie.test = FALSE,
plotHistogram = FALSE,
modules = list(
early = modules[[1]],
mid = modules[[2]],
late = modules[[3]]
),
runs = NULL
)
}
p.vals_vec[i] <- rht$p.value
if (lillie.test)
lillie_vec[i] <-
rht$lillie.test
# if(runs >= 10){
# # printing out the progress
# setTxtProgressBar(progressBar,i)
# }
}
}
#cat("\n")
graphics::plot(
x = p.vals_vec,
type = "l" ,
lwd = 6,
ylim = c(0, 1),
col = "darkblue",
xlab = "Runs",
ylab = "p-value"
)
graphics::abline(h = 0.05,
lty = 2,
lwd = 3)
if (lillie.test) {
tbl <- table(factor(lillie_vec, levels = c("FALSE", "TRUE")))
graphics::barplot(
height = tbl / sum(tbl),
beside = TRUE,
names.arg = c("FALSE", "TRUE"),
ylab = "Relative Frequency",
main = paste0("runs = ", runs)
)
}
}
#if(real_score >= 0)
pval <-
stats::pnorm(
real_score,
mean = mu,
sd = sigma,
lower.tail = FALSE
)
#if(real_score < 0)
#pval <- pnorm(real_score,mean=mu,sd=sigma,lower.tail=TRUE)
### computing the standard deviation of the sampled TAI values for each stage separately
sd_vals <- vector(mode = "numeric", length = nCols - 2)
sd_vals <- apply(resMatrix, 2, stats::sd)
if (lillie.test) {
# perform Lilliefors K-S-Test
lillie_p.val <-
nortest::lillie.test(score_vector)$p.value
# does the Lilliefors test pass the criterion
lillie_bool <- (lillie_p.val > 0.05)
if (gof.warning &
(lillie_p.val < 0.05) &
(plotHistogram == FALSE)) {
warning(
"Lilliefors (Kolmogorov-Smirnov) test for normality did not pass the p > 0.05 criterion!"
)
}
}
if (lillie.test)
return(list(
p.value = pval,
std.dev = sd_vals,
lillie.test = lillie_bool
))
if (!lillie.test)
return(list(
p.value = pval,
std.dev = sd_vals,
lillie.test = NA
))
}
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