From 8092a9989917104744098eead7cd441047c46df7 Mon Sep 17 00:00:00 2001
From: noriakis <31095487+noriakis@users.noreply.github.com>
Date: Tue, 22 Oct 2024 22:41:37 +0900
Subject: [PATCH] doc updates

---
 NAMESPACE                         |  1 +
 R/NMF.R                           | 18 ++++++++++++------
 R/utils.R                         |  7 +++++--
 man/plotAbundanceWithinSpecies.Rd |  5 ++++-
 man/plotStackedBarPlot.Rd         |  6 ++++--
 man/scaler.NNLM.Rd                | 19 +++++++++++++++++++
 6 files changed, 45 insertions(+), 11 deletions(-)
 create mode 100644 man/scaler.NNLM.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 3607c8d..d0e7f6e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -68,6 +68,7 @@ export(plotStackedBarPlot)
 export(rankComponents)
 export(returnGenes)
 export(reverseAnnot)
+export(scaler.NNLM)
 export(setAnnotation)
 export(setGroup)
 export(setMap)
diff --git a/R/NMF.R b/R/NMF.R
index 824082e..250518a 100644
--- a/R/NMF.R
+++ b/R/NMF.R
@@ -181,10 +181,11 @@ NMF <- function(stana, species, rank=3, target="kos", seed=53, method="snmf/r",
 #' 
 #' @param stana stana boject
 #' @param sp species
-#' @param by "NMF" or "coef"
+#' @param by "NMF", "manual", or "coef"
+#' @param mat manual matrix
 #' @return ggplot
 #' @export
-plotStackedBarPlot <- function(stana, sp, by="NMF") {
+plotStackedBarPlot <- function(stana, sp, by="NMF", mat=NULL) {
 	if (is.null(stana@NMF[[sp]]) & is.null(stana@coefMat[[sp]])) {
 		stop("NMF results or coefficient matrix should be set")
 	}
@@ -193,7 +194,9 @@ plotStackedBarPlot <- function(stana, sp, by="NMF") {
         coefMat <- coef(res)	
 	} else if (by=="coef") {
 		coefMat <- stana@coefMat[[sp]]
-	} else {
+	} else if (by=="manual") {
+        coefMat <- mat
+    } else {
 		stop("NMF results or coefficient matrix should be set")
 	}
     relab <- apply(coefMat, 2, function(x) x / sum(x))
@@ -261,9 +264,10 @@ alphaDiversityWithinSpecies <- function(stana, species, method="shannon", rank=5
 #' @param tss perform total sum scaling
 #' @param return_data return only the data, not plot
 #' @param by NMF or coef matrix set to `coefMat` slot
+#' @param mat matrix (row factor column sample) of H
 #' @export
 #' @return ggplot object
-plotAbundanceWithinSpecies <- function(stana, species, tss=TRUE, return_data=FALSE, by="NMF") {
+plotAbundanceWithinSpecies <- function(stana, species, tss=TRUE, return_data=FALSE, by="NMF", mat=NULL) {
 	if (by=="NMF") {
 	    if (is.null(stana@NMF[[species]])) {
 	        stana <- NMF(stana, species)
@@ -272,8 +276,10 @@ plotAbundanceWithinSpecies <- function(stana, species, tss=TRUE, return_data=FAL
         H <- coef(res)	
 	} else if (by=="coef") {
 		H <- stana@coefMat[[species]]
-	} else {
-		stop("NMF or coef should be specified in `by`")
+	} else if (by=="manual") {
+        H <- mat
+    } else {
+		stop("NMF, manual, or coef should be specified in `by`")
 	}
 
     if (tss) {
diff --git a/R/utils.R b/R/utils.R
index dba3b08..7f18f89 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -33,8 +33,11 @@ setGroup <- function(stana, cl) {
 }
 
 
-
-#' @noRd
+#' scaler.NNLM
+#' @param nmf NNLM object
+#' @param target coef or basis
+#' @export
+#' @return list
 scaler.NNLM <- function(nmf, target="coef") {
     if (target=="basis") {
         scaledW <- apply(nmf$W, 2, function(x) x / sum(x))
diff --git a/man/plotAbundanceWithinSpecies.Rd b/man/plotAbundanceWithinSpecies.Rd
index 691e281..8bb5a9b 100644
--- a/man/plotAbundanceWithinSpecies.Rd
+++ b/man/plotAbundanceWithinSpecies.Rd
@@ -9,7 +9,8 @@ plotAbundanceWithinSpecies(
   species,
   tss = TRUE,
   return_data = FALSE,
-  by = "NMF"
+  by = "NMF",
+  mat = NULL
 )
 }
 \arguments{
@@ -22,6 +23,8 @@ plotAbundanceWithinSpecies(
 \item{return_data}{return only the data, not plot}
 
 \item{by}{NMF or coef matrix set to `coefMat` slot}
+
+\item{mat}{matrix (row factor column sample) of H}
 }
 \value{
 ggplot object
diff --git a/man/plotStackedBarPlot.Rd b/man/plotStackedBarPlot.Rd
index 61e302e..475f536 100644
--- a/man/plotStackedBarPlot.Rd
+++ b/man/plotStackedBarPlot.Rd
@@ -4,14 +4,16 @@
 \alias{plotStackedBarPlot}
 \title{plotStackedBarPlot}
 \usage{
-plotStackedBarPlot(stana, sp, by = "NMF")
+plotStackedBarPlot(stana, sp, by = "NMF", mat = NULL)
 }
 \arguments{
 \item{stana}{stana boject}
 
 \item{sp}{species}
 
-\item{by}{"NMF" or "coef"}
+\item{by}{"NMF", "manual", or "coef"}
+
+\item{mat}{manual matrix}
 }
 \value{
 ggplot
diff --git a/man/scaler.NNLM.Rd b/man/scaler.NNLM.Rd
new file mode 100644
index 0000000..5fb2c33
--- /dev/null
+++ b/man/scaler.NNLM.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{scaler.NNLM}
+\alias{scaler.NNLM}
+\title{scaler.NNLM}
+\usage{
+scaler.NNLM(nmf, target = "coef")
+}
+\arguments{
+\item{nmf}{NNLM object}
+
+\item{target}{coef or basis}
+}
+\value{
+list
+}
+\description{
+scaler.NNLM
+}