From 4dadbc168f3dd4d188bb78302ced22abf6653418 Mon Sep 17 00:00:00 2001
From: ningbioinfo <ning.liu@adelaide.edu.au>
Date: Tue, 13 Aug 2024 10:33:24 +0930
Subject: [PATCH] new fun: perplexityPermute

---
 NAMESPACE                |  1 +
 R/calc_metrics.R         | 74 ++++++++++++++++++++++++++++++++++++++++
 man/perplexityPermute.Rd | 44 ++++++++++++++++++++++++
 3 files changed, 119 insertions(+)
 create mode 100644 man/perplexityPermute.Rd

diff --git a/NAMESPACE b/NAMESPACE
index e46daf6..bc5465e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,6 +5,7 @@ export(clustByHood)
 export(findNearCells)
 export(mergeByGroup)
 export(mergeHoodSpe)
+export(perplexityPermute)
 export(plotColocal)
 export(plotHoodMat)
 export(plotProbDist)
diff --git a/R/calc_metrics.R b/R/calc_metrics.R
index f22e316..247d628 100644
--- a/R/calc_metrics.R
+++ b/R/calc_metrics.R
@@ -63,3 +63,77 @@ calcMetrics <- function(spe, pm = NA, pm_cols = NA,
 
   return(spe)
 }
+
+.get_perplexity <- function(pm){
+    p <- calculate_metrics(pm)[,"perplexity"]
+    return(p)
+}
+
+#' Compute p-value for perplexity via permutation
+#'
+#' @param spe A SpatialExperiment object.
+#' @param pm Optional. The probability matrix.
+#' @param pm_cols The colnames of probability matrix. This is requires for
+#' SpatialExperiment input. Assuming that the probability is 
+#' stored in the colData.
+#' @param n_perm Integer number. The number of permutation. 1000 by default.
+#'
+#' @return A SpatialExperiment object. Calculated P-value and adjusted P-value
+#' are saved as columns in the colData of the SpatialExperiment object.
+#' P-value and adjusted P-value are calculated based on permutation test and 
+#' Benjamini Hochberg correction.
+#' 
+#' @export
+#'
+#' @examples
+#'
+#' data("spe_test")
+#'
+#' spe <- readHoodData(spe, anno_col = "celltypes")
+#'
+#' fnc <- findNearCells(spe, k = 100)
+#'
+#' pm <- scanHoods(fnc$distance)
+#'
+#' pm2 <- mergeByGroup(pm, fnc$cells)
+#'
+#' spe <- mergeHoodSpe(spe, pm2)
+#'
+#' spe <- perplexityPermute(spe, pm_cols = colnames(pm2))
+perplexityPermute <- function(spe, pm = NA, pm_cols = NA, n_perm = 1000) {
+    if (!is(spe, "SpatialExperiment")){
+        stop("The input spe must be a SpatialExperiment object.")
+    }
+    if (is(pm, "logical")) {
+        if (is(pm_cols, "logical")) {
+            stop("Need to input either the pm or pm_cols parameters.")
+        } else {
+            pm <- as.data.frame(colData(spe), 
+                                optional = TRUE)[, pm_cols] |>
+                as.matrix()
+        }
+    } else {
+        pm <- pm
+    }
+    
+    observed_perplexity <- .get_perplexity(pm)
+
+    permuted_perplexities <- matrix(NA, nrow(pm), n_perm)
+    
+    for (i in 1:n_perm) {
+        permuted_matrix <- pm[sample(1:nrow(pm)), ]
+        permuted_perplexities[, i] <- .get_perplexity(permuted_matrix)
+    }
+    
+    p_values <- apply(as.matrix(observed_perplexity), 1, function(obs) {
+        mean(permuted_perplexities >= obs)
+    })
+    
+    adjp <- stats::p.adjust(p_values, method = "BH")
+    
+    colData(spe)[,"perplexity_p"] <- p_values
+    colData(spe)[,"perplexity_adjp"] <- adjp
+    
+    return(spe)
+}
+
diff --git a/man/perplexityPermute.Rd b/man/perplexityPermute.Rd
new file mode 100644
index 0000000..668965f
--- /dev/null
+++ b/man/perplexityPermute.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calc_metrics.R
+\name{perplexityPermute}
+\alias{perplexityPermute}
+\title{Compute p-value for perplexity via permutation}
+\usage{
+perplexityPermute(spe, pm = NA, pm_cols = NA, n_perm = 1000)
+}
+\arguments{
+\item{spe}{A SpatialExperiment object.}
+
+\item{pm}{Optional. The probability matrix.}
+
+\item{pm_cols}{The colnames of probability matrix. This is requires for
+SpatialExperiment input. Assuming that the probability is
+stored in the colData.}
+
+\item{n_perm}{Integer number. The number of permutation. 1000 by default.}
+}
+\value{
+A SpatialExperiment object. Calculated P-value and adjusted P-value
+are saved as columns in the colData of the SpatialExperiment object.
+P-value and adjusted P-value are calculated based on permutation test and
+Benjamini Hochberg correction.
+}
+\description{
+Compute p-value for perplexity via permutation
+}
+\examples{
+
+data("spe_test")
+
+spe <- readHoodData(spe, anno_col = "celltypes")
+
+fnc <- findNearCells(spe, k = 100)
+
+pm <- scanHoods(fnc$distance)
+
+pm2 <- mergeByGroup(pm, fnc$cells)
+
+spe <- mergeHoodSpe(spe, pm2)
+
+spe <- perplexityPermute(spe, pm_cols = colnames(pm2))
+}