--- a
+++ b/singlecellmultiomics/bamProcessing/bamPlateVisualisation.py
@@ -0,0 +1,50 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+from singlecellmultiomics.statistic import PlateStatistic
+import singlecellmultiomics.modularDemultiplexer
+import math
+import string
+import pandas as pd
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import sys
+import pysam
+import collections
+import argparse
+from singlecellmultiomics.tagtools import tagtools
+import pysamiterators.iterators as pysamIterators
+import gzip
+import pickle
+import subprocess
+
+import matplotlib
+import matplotlib.lines as mlines
+matplotlib.rcParams['figure.dpi'] = 160
+matplotlib.use('Agg')
+TagDefinitions = singlecellmultiomics.modularDemultiplexer.TagDefinitions
+
+
+if __name__ == '__main__':
+    argparser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description='Visualize single cell statistics on a plate plot')
+    argparser.add_argument(
+        '-o',
+        type=str,
+        help="output plot folder path, every library will be visualised as a separate plate",
+        default='./plots/')
+
+    argparser.add_argument('alignmentfiles', type=str, nargs='*')
+    args = argparser.parse_args()
+
+    if not os.path.exists(args.o):
+        os.makedirs(args.o)
+
+    ps = PlateStatistic(args)
+    for alignmentFile in args.alignmentfiles:
+        with pysam.AlignmentFile(alignmentFile) as f:
+            for read in f:
+                ps.processRead(read)
+
+    ps.plot(args.o + '/PS')