From 2c75ca2e4d10350b92c47c68af517c50a30e2ab8 Mon Sep 17 00:00:00 2001
From: cweng <cweng@c3b15.wi.mit.edu>
Date: Sun, 12 Nov 2023 22:58:52 -0500
Subject: [PATCH] added back mitoTracing() for Create_mitoTracing

---
 NAMESPACE                |  2 ++
 R/BuidTree.R             | 35 ++++++++++++++++++++++++++++++++++-
 man/mitoTracing-class.Rd | 38 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 74 insertions(+), 1 deletion(-)
 create mode 100644 man/mitoTracing-class.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 756c698..1f4c9df 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -55,6 +55,7 @@ export(Translate_simple_RNA2ATAC)
 export(Vfilter_v3)
 export(Vfilter_v4)
 export(convert_mitotracing_redeemR)
+export(mitoTracing)
 export(plot_depth)
 export(plot_depth_legacy)
 export(plot_npSummary)
@@ -68,6 +69,7 @@ export(redeemR.read)
 exportClasses(Datatoplots)
 exportClasses(DistObjects)
 exportClasses(TREE)
+exportClasses(mitoTracing)
 exportClasses(redeemR)
 exportMethods(AddDatatoplot_clustering)
 exportMethods(AddDist)
diff --git a/R/BuidTree.R b/R/BuidTree.R
index 7f16023..e644f36 100755
--- a/R/BuidTree.R
+++ b/R/BuidTree.R
@@ -89,6 +89,39 @@ redeemR<-setClass(
            )
 )
 
+#' Legacy function: Major mitoTracing class that store clonal-resolved multi-omics
+#'
+#' @slot GTsummary.filtered  The Mitochondrial genotype data frame
+#' @slot CellMeta Store meta data for each cell type
+#' @slot V.fitered.list a list of data frame of variant metrics, VAF, cellN, etc (each for different stringency),
+#' @slot UniqueV A character showing the number of usable variant
+#' @slot Cts.Mtx A sparse matrix cell-mitoVariants, store the variant count
+#' @slot Cts.Mtx.bi A sparse matrix cell-mitoVariants, The variant count has been binarized into 0 and 1
+#' @slot Ctx.Mtx.depth A sparse matrix cell-mitoVariants(total counts for each position), store the variant count
+#' @slot para A character showing the parameter of this object
+#' @slot Seurat Seurat object storing the clonal clustering results
+#' @slot DataToplotList The customized class of Datatoplots: A list of dataframe for further plotting
+#' @slot DistObjects The customized class that stores the cell-cell distances
+#' @slot TREE The customized class that wraps phylogenetic tree
+#' @import Seurat
+#' @export
+mitoTracing<-setClass(
+    "mitoTracing",
+    slots=c(GTsummary.filtered="data.frame",
+            CellMeta="data.frame",
+            V.fitered.list="list",
+            UniqueV="character",
+            Cts.Mtx="dgCMatrix",
+            Cts.Mtx.bi="dgCMatrix",
+            Ctx.Mtx.depth="matrix",
+            para="character",
+            Seurat="Seurat",
+            DataToplotList="Datatoplots",
+            DistObjects="DistObjects",
+            TREE="TREE",
+            AssignedVariant="list"
+           )
+)
 
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # Class definitions
@@ -660,7 +693,7 @@ V.fitered.list<-c(V.fitered.list,list(V.filtered))
 V.union.unique<-unique(V.union)
 names(V.fitered.list)<-labels
 GTsummary.all.filtered<-subset(GTsummary.all,Variants %in% V.union.unique & Cell %in% CellMeta.all$Cell)
-ob<-redeemR()
+ob<-mitoTracing()
 ob@GTsummary.filtered<-GTsummary.all.filtered
 ob@CellMeta<-CellMeta.all
 ob@V.fitered.list=V.fitered.list
diff --git a/man/mitoTracing-class.Rd b/man/mitoTracing-class.Rd
new file mode 100644
index 0000000..c92d213
--- /dev/null
+++ b/man/mitoTracing-class.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/BuidTree.R
+\docType{class}
+\name{mitoTracing-class}
+\alias{mitoTracing-class}
+\alias{mitoTracing}
+\title{Legacy function: Major mitoTracing class that store clonal-resolved multi-omics}
+\description{
+Legacy function: Major mitoTracing class that store clonal-resolved multi-omics
+}
+\section{Slots}{
+
+\describe{
+\item{\code{GTsummary.filtered}}{The Mitochondrial genotype data frame}
+
+\item{\code{CellMeta}}{Store meta data for each cell type}
+
+\item{\code{V.fitered.list}}{a list of data frame of variant metrics, VAF, cellN, etc (each for different stringency),}
+
+\item{\code{UniqueV}}{A character showing the number of usable variant}
+
+\item{\code{Cts.Mtx}}{A sparse matrix cell-mitoVariants, store the variant count}
+
+\item{\code{Cts.Mtx.bi}}{A sparse matrix cell-mitoVariants, The variant count has been binarized into 0 and 1}
+
+\item{\code{Ctx.Mtx.depth}}{A sparse matrix cell-mitoVariants(total counts for each position), store the variant count}
+
+\item{\code{para}}{A character showing the parameter of this object}
+
+\item{\code{Seurat}}{Seurat object storing the clonal clustering results}
+
+\item{\code{DataToplotList}}{The customized class of Datatoplots: A list of dataframe for further plotting}
+
+\item{\code{DistObjects}}{The customized class that stores the cell-cell distances}
+
+\item{\code{TREE}}{The customized class that wraps phylogenetic tree}
+}}
+