From 826b45016aeeeea34ddc2f2daa272962a556f726 Mon Sep 17 00:00:00 2001
From: noriakis <31095487+noriakis@users.noreply.github.com>
Date: Sat, 30 Mar 2024 07:19:55 +0900
Subject: [PATCH] dist

---
 NAMESPACE       |  1 +
 R/plotDist.R    | 58 +++++++++++++++++++++++++++++++++++++++++++++++++
 man/plotDist.Rd | 39 +++++++++++++++++++++++++++++++++
 3 files changed, 98 insertions(+)
 create mode 100644 R/plotDist.R
 create mode 100644 man/plotDist.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 1bd6621..261f777 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -55,6 +55,7 @@ export(pathwayWithFactor)
 export(plotAbundanceWithinSpecies)
 export(plotCirclize)
 export(plotCoverage)
+export(plotDist)
 export(plotGenes)
 export(plotHeatmap)
 export(plotKEGGPathway)
diff --git a/R/plotDist.R b/R/plotDist.R
new file mode 100644
index 0000000..e06526c
--- /dev/null
+++ b/R/plotDist.R
@@ -0,0 +1,58 @@
+#'
+#' plotDist
+#' 
+#' Perform distance calculation based on the matrix
+#' stored in stana, and plot the heatmap with grouping
+#' information
+#' 
+#' @param stana stana object
+#' @param sp species to be examined
+#' @param cl named list of samples
+#' @param target tree, snps, genes, kos, fasta
+#' @param AAfunc if choose `fasta`, provide function for calculating distance
+#' @param AAargs provided to `AAfunc`
+#' @param distMethod distance method passed to dist() (default, manhattan)
+#' @param distArg passed to `dist()
+#' @export
+plotDist <- function(stana, sp, cl=NULL, AAfunc=dist.ml, AAargs=list(),
+    target="snps", distMethod="manhattan", distArg=list()) {
+      if (is.null(cl)) {cl <- stana@cl}
+      if (length(sp)>1) {stop("Please specify one species")}
+        cat_subtle("# Performing dist in ", sp, " target is ", target, "\n", sep="")
+        if (target=="snps") {
+            snps <- stana@snps[[sp]]
+            if (!is.null(stana@includeSNVID[[sp]])) {
+                cat_subtle("# The set SNV ID information (", length(stana@includeSNVID[[sp]]), ") is used.\n")
+                snps <- snps[stana@includeSNVID[[sp]], ]
+            }
+            ## Replace zero depth with NA
+            snps[snps == -1] <- NA
+        } else if (target=="tree") {
+            if (!is.null(stana@treeList[[sp]])) {
+              tre <- stana@treeList[[sp]]
+              ## cophenetic distance
+              d <- as.dist(ape::cophenetic.phylo(tre))
+              sn <- attr(d, "Labels")
+            } else {
+              stop("No tree found in stana@treeList")
+            }
+        } else if (target=="fasta") {
+          AAargs[["x"]] <- stana@fastaList[[sp]]
+          d <- do.call(AAfunc, AAargs)
+          sn <- attr(d, "Labels")
+        } else if (target=="kos") {
+            snps <- stana@kos[[sp]]          
+        } else {
+            snps <- stana@genes[[sp]]
+        }
+
+        if (!(target %in% c("tree","fasta"))) {
+          distArg[["x"]] <- t(snps)
+          distArg[["method"]] <- distMethod
+          d <- do.call(dist, distArg)
+          sn <- attr(d, "Labels")      
+        }
+        met <- data.frame(listToNV(cl))
+        met <- data.frame(met[sn, ]) %>% `row.names<-`(sn)
+        pheatmap(d, annotation_row=met)
+}
\ No newline at end of file
diff --git a/man/plotDist.Rd b/man/plotDist.Rd
new file mode 100644
index 0000000..ba1f613
--- /dev/null
+++ b/man/plotDist.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotDist.R
+\name{plotDist}
+\alias{plotDist}
+\title{plotDist}
+\usage{
+plotDist(
+  stana,
+  sp,
+  cl = NULL,
+  AAfunc = dist.ml,
+  AAargs = list(),
+  target = "snps",
+  distMethod = "manhattan",
+  distArg = list()
+)
+}
+\arguments{
+\item{stana}{stana object}
+
+\item{sp}{species to be examined}
+
+\item{cl}{named list of samples}
+
+\item{AAfunc}{if choose `fasta`, provide function for calculating distance}
+
+\item{AAargs}{provided to `AAfunc`}
+
+\item{target}{tree, snps, genes, kos, fasta}
+
+\item{distMethod}{distance method passed to dist() (default, manhattan)}
+
+\item{distArg}{passed to `dist()}
+}
+\description{
+Perform distance calculation based on the matrix
+stored in stana, and plot the heatmap with grouping
+information
+}