From 3ae6030f2319ea0879c08583b08f92c404f3ca0e Mon Sep 17 00:00:00 2001
From: Frank Cheng <zhangc518@gmail.com>
Date: Thu, 13 Dec 2018 15:12:46 -0800
Subject: [PATCH 1/3] typos in readme

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 73e0d05..e1cd34f 100644
--- a/README.md
+++ b/README.md
@@ -51,7 +51,7 @@ cut -f 1 example/example.r5.n1/example.r5.n1.box.sta | sed "1 s/contributes/rank
 for i in `seq 5 20`;
 do echo $i;
 n=1
-prefix=example.r${i}.n\${n}
+prefix=example.r${i}.n{n}
 
 # calculate cell sparseness and entropy using the statH file
 Rscript snATAC.statBox.R -i example/$prefix/$prefix.statH -o example/$prefix/$prefix >> example/$prefix/$prefix.sta.txt
@@ -77,7 +77,7 @@ done;
 for i in `seq 5 20`;
 do echo $i;
 n=1
-prefix=example.r${i}.n\${n}
+prefix=example.r${i}.n{n}
 awk -v a=${i} 'BEGIN{FS=OFS="\t"}{print "r"a".c"$4*1}' example/$prefix/$prefix.statH > example/$prefix/$prefix.statH.tmp
 done;
 
@@ -85,8 +85,8 @@ for j in `seq 5 19`;
 do echo $j;
 j1=`bc <<< ${j}+1`
 echo ${j1}
-prefix1=example.r${j}.n\${n}
-prefix2=example.r${j1}.n\${n}
+prefix1=example.r${j}.n{n}
+prefix2=example.r${j1}.n{n}
 paste example/$prefix1/$prefix1.statH.tmp example/$prefix2/$prefix2.statH.tmp | sort | uniq -c | awk 'BEGIN{OFS="\t"}{print $2,$3,$1}' >> example/example.statH.sankey.summary
 done;
 rm -rf example/*/*.statH.tmp

From 22995ec0fa4bf5ed5606a7ffd1201cde3ea0cb77 Mon Sep 17 00:00:00 2001
From: Frank Cheng <zhangc518@gmail.com>
Date: Thu, 13 Dec 2018 15:18:50 -0800
Subject: [PATCH 2/3] avoid cases that many 0 features

---
 snATAC.nmf.lite.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/snATAC.nmf.lite.py b/snATAC.nmf.lite.py
index db31139..ea9db9c 100644
--- a/snATAC.nmf.lite.py
+++ b/snATAC.nmf.lite.py
@@ -127,7 +127,7 @@ def filter_V(V, xgi, ygi, prob, ct):
 
 	rowSum = np.sum(newV,axis=1)
 	rowQ = mquantiles(np.array(rowSum), prob=prob)
-	row_tokeep = ravel(rowSum >= rowQ)
+	row_tokeep = ravel(rowSum > rowQ)
 	newV = newV[row_tokeep, :]
 	selt_xgi = list(compress(xgi, col_tokeep))
 	selt_ygi = list(compress(ygi, row_tokeep))

From 8bf13aed00a6839bf2d9cdc228c5e83e7e6f3f8d Mon Sep 17 00:00:00 2001
From: Frank Cheng <zhangc518@gmail.com>
Date: Thu, 13 Dec 2018 15:20:52 -0800
Subject: [PATCH 3/3] requirment

---
 requirements.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/requirements.txt b/requirements.txt
index 5a7b8f7..126552b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
+#python3
 matplotlib
 fastcluster
 pysam
@@ -9,3 +10,4 @@ sklearn
 pybedtools
 multiprocessing
 pandas
+colorlover