From c55fdd1343d4b76d1bfdff85ae3b67e3738808d5 Mon Sep 17 00:00:00 2001
From: Konstantin Pelz <35631987+PelzKo@users.noreply.github.com>
Date: Fri, 23 Jul 2021 14:26:21 +0200
Subject: [PATCH 1/3] Method now works even with one bulk sample

---
 R/utils.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 08a6cda..dd18706 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -156,7 +156,7 @@ music_prop = function(bulk.eset, sc.eset, markers = NULL, clusters, samples, sel
     names(M.S) <- my_ms_names
   }
   
-  Yjg = relative.ab(exprs(bulk.eset)[m.bulk, ]); N.bulk = ncol(bulk.eset);
+  Yjg = relative.ab(exprs(bulk.eset)[m.bulk, , drop = FALSE]); N.bulk = ncol(bulk.eset);
   if(ct.cov){
     Sigma.ct = sc.basis$Sigma.ct[, m.sc];
     
@@ -299,7 +299,7 @@ music_prop.cluster = function(bulk.eset, sc.eset, group.markers, groups, cluster
   cluster.diff = unique(unlist(group.markers))
   
   D1.cluster = cluster.sc.basis$Disgn.mtx[cluster.select, ]; M.S.cluster = cluster.sc.basis$M.S;
-  Yjg = relative.ab(exprs(bulk.eset)[m.bulk, ]); N.bulk = ncol(bulk.eset);
+  Yjg = relative.ab(exprs(bulk.eset)[m.bulk, , drop = FALSE]); N.bulk = ncol(bulk.eset);
   
   Sigma.cluster = cluster.sc.basis$Sigma[cluster.select, ];
   

From 365c35e269c76fbb905898ecf9f19868ab38b346 Mon Sep 17 00:00:00 2001
From: Konstantin Pelz <35631987+PelzKo@users.noreply.github.com>
Date: Wed, 18 Aug 2021 20:38:26 +0200
Subject: [PATCH 2/3] added import to method because it would not find exprs
 when music_prop is called

---
 R/utils.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/utils.R b/R/utils.R
index dd18706..2185c1d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -117,6 +117,8 @@ get_upper_tri = function(cormat){
 #' @seealso
 #' \code{\link{music_basis}}
 #' @export
+#' 
+#' @importFrom Biobase exprs pData
 music_prop = function(bulk.eset, sc.eset, markers = NULL, clusters, samples, select.ct = NULL, cell_size = NULL, ct.cov = FALSE, verbose = TRUE,
                       iter.max = 1000, nu = 0.0001, eps = 0.01, centered = FALSE, normalize = FALSE, ... ){
   bulk.gene = rownames(bulk.eset)[rowMeans(exprs(bulk.eset)) != 0]

From fc1667f2cf10bcf906e7f724c02d4cc354a584b2 Mon Sep 17 00:00:00 2001
From: Konstantin Pelz <35631987+PelzKo@users.noreply.github.com>
Date: Wed, 18 Aug 2021 20:50:31 +0200
Subject: [PATCH 3/3] reverting last commit, extra import not needed

---
 R/utils.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 2185c1d..dd18706 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -117,8 +117,6 @@ get_upper_tri = function(cormat){
 #' @seealso
 #' \code{\link{music_basis}}
 #' @export
-#' 
-#' @importFrom Biobase exprs pData
 music_prop = function(bulk.eset, sc.eset, markers = NULL, clusters, samples, select.ct = NULL, cell_size = NULL, ct.cov = FALSE, verbose = TRUE,
                       iter.max = 1000, nu = 0.0001, eps = 0.01, centered = FALSE, normalize = FALSE, ... ){
   bulk.gene = rownames(bulk.eset)[rowMeans(exprs(bulk.eset)) != 0]