--- a
+++ b/aggmap/utils/vismap.py
@@ -0,0 +1,209 @@
+from scipy.cluster.hierarchy import dendrogram, linkage, to_tree
+from scipy.spatial.distance import squareform
+import seaborn as sns
+from highcharts import Highchart
+import pandas as pd
+import numpy as np
+import os
+
+from aggmap.utils.logtools import print_info
+
+
+def plot_scatter(mp, htmlpath = './', htmlname = None, radius = 2, enabled_data_labels = False):
+    '''
+    mp: the object of mp
+    htmlpath: the figure path, not include the prefix of 'html'
+    htmlname: the name 
+    radius: int, defaut:3, the radius of scatter dot
+    '''
+    
+    title = '2D emmbedding of %s based on %s method' % (mp.ftype, mp.emb_method)
+    subtitle = 'number of %s: %s, metric method: %s' % (mp.ftype, len(mp.flist), mp.metric)
+    name = '%s_%s_%s_%s_%s' % (mp.ftype,len(mp.flist), mp.metric, mp.emb_method, 'scatter')
+    
+    if not os.path.exists(htmlpath):
+        os.makedirs(htmlpath)
+    
+    if htmlname:
+        name = htmlname + '_' + name 
+        
+    filename = os.path.join(htmlpath, name)
+    print_info('generate file: %s' % filename)
+
+    colormaps = mp.colormaps
+    df = mp.df_scatter
+
+    H = Highchart(width=1000, height=850)
+    H.set_options('chart', {'type': 'scatter', 'zoomType': 'xy'})    
+    H.set_options('title', {'text': title})
+    H.set_options('subtitle', {'text': subtitle})
+    H.set_options('xAxis', {'title': {'enabled': True,'text': 'X', 'style':{'fontSize':20}},
+                           'labels':{'style':{'fontSize':20}}, 
+                           'gridLineWidth': 1,
+                           'startOnTick': True,
+                           'endOnTick': True,
+                           'showLastLabel': True})
+    
+    H.set_options('yAxis', {'title': {'text': 'Y', 'style':{'fontSize':20}},
+                            'labels':{'style':{'fontSize':20}}, 
+                            'gridLineWidth': 1,})
+    
+#     H.set_options('legend', {'layout': 'horizontal','verticalAlign': 'top','align':'right','floating': False,
+#                              'backgroundColor': "(Highcharts.theme && Highcharts.theme.legendBackgroundColor) || '#FFFFFF'",
+#                              'borderWidth': 1})
+    
+    
+    H.set_options('legend', {'align': 'right', 'layout': 'vertical',
+                             'margin': 1, 'verticalAlign': 'top', 'y':40,
+                              'symbolHeight': 12, 'floating': False,})
+
+    
+    H.set_options('plotOptions', {'scatter': {'marker': {'radius': radius,
+                                                         'states': {'hover': {'enabled': True,
+                                                                              'lineColor': 'rgb(100,100,100)'}}},
+                                              'states': {'hover': {'marker': {'enabled': False} }},
+                                              'tooltip': {'headerFormat': '<b>{series.name}</b><br>',
+                                                          'pointFormat': '{point.IDs}'}},
+                                  'series': {'turboThreshold': 5000, 
+                                             'dataLabels': {'enabled': enabled_data_labels, 'format': '{point.IDs}'}}
+                                 })
+    
+    for subtype, color in colormaps.items():
+        dfi = df[df['Subtypes'] == subtype]
+        if len(dfi) == 0:
+            continue
+            
+        data = dfi.to_dict('records')
+        H.add_data_set(data, 'scatter', subtype, color=color)
+    H.save_file(filename)
+    print_info('save html file to %s' % filename)
+    return H
+
+
+
+def plot_grid(mp, htmlpath = './', htmlname = None, enabled_data_labels = False):
+    '''
+    mp: the object of mp
+    htmlpath: the figure path
+    '''    
+
+    if not os.path.exists(htmlpath):
+        os.makedirs(htmlpath)    
+    
+    title = 'Assignment of %s by %s emmbedding result' % (mp.ftype, mp.emb_method)
+    subtitle = 'number of %s: %s, metric method: %s' % (mp.ftype, len(mp.flist), mp.metric)    
+
+    name = '%s_%s_%s_%s_%s' % (mp.ftype,len(mp.flist), mp.metric, mp.emb_method, 'mp')
+    
+    if htmlname:
+        name = name = htmlname + '_' + name   
+    
+    filename = os.path.join(htmlpath, name)
+    print_info('generate file: %s' % filename)
+
+    colormaps = mp.colormaps
+    df = mp.df_grid
+    
+    H = Highchart(width=1000, height=850)
+    H.set_options('chart', {'type': 'heatmap', 'zoomType': 'xy'})
+    H.set_options('title', {'text': title})
+    H.set_options('subtitle', {'text': subtitle})
+#     H.set_options('xAxis', {'title': '', 
+#                             'min': 0, 'max': mp._S.fmap_shape[1]-1,
+#                             'allowDecimals':False,
+#                             'labels':{'style':{'fontSize':20}}})
+    
+#     H.set_options('yAxis', {'title': '', 'tickPosition': 'inside', 
+#                             'min': 0, 'max': mp._S.fmap_shape[0]-1,
+#                             'reversed': True,
+#                             'allowDecimals':False,
+#                             'labels':{'style':{'fontSize':20}}})
+
+    H.set_options('xAxis', {'title': None,                         
+                            'min': 0, 'max': mp.fmap_shape[1]-1,
+                            'startOnTick': False,
+                            'endOnTick': False,    
+                            'allowDecimals':False,
+                            'labels':{'style':{'fontSize':20}}})
+
+    
+    H.set_options('yAxis', {'title': {'text': ' ', 'style':{'fontSize':20}}, 
+                            'startOnTick': False,
+                            'endOnTick': False,
+                            'gridLineWidth': 0,
+                            'reversed': True,
+                            'min': 0, 'max': mp.fmap_shape[0]-1,
+                            'allowDecimals':False,
+                            'labels':{'style':{'fontSize':20}}})
+    
+
+
+    H.set_options('legend', {'align': 'right', 'layout': 'vertical',
+                             'margin': 1, 'verticalAlign': 'top', 
+                             'y': 60, 'symbolHeight': 12, 'floating': False,})
+
+    
+    H.set_options('tooltip', {'headerFormat': '<b>{series.name}</b><br>',
+                              'pointFormat': '{point.v}'})
+
+    
+    H.set_options('plotOptions', {'series': {'turboThreshold': 5000,
+                                             'dataLabels': {'enabled': enabled_data_labels, 
+                                                            'format': '{point.v}',
+                                                            'style': {'textOutline':False, 'color': 'black'},
+
+                                                           }
+                                            }
+                                 }
+                 )
+    
+    for subtype, color in colormaps.items():
+        dfi = df[df['Subtypes'] == subtype]
+        if len(dfi) == 0:
+            continue
+        H.add_data_set(dfi.to_dict('records'), 'heatmap', 
+                       name = subtype,
+                       #dataLabels = {'enabled': True, 'color': color}
+                       color = color,
+                      )
+    H.save_file(filename)
+    print_info('save html file to %s' % filename)
+    
+    return H
+
+
+
+
+
+
+def _getNewick(node, newick, parentdist, leaf_names):
+    if node.is_leaf():
+        return "%s:%.2f%s" % (leaf_names[node.id], parentdist - node.dist, newick)
+    else:
+        if len(newick) > 0:
+            newick = "):%.2f%s" % (parentdist - node.dist, newick)
+        else:
+            newick = ");"
+        newick = _getNewick(node.get_left(), newick, node.dist, leaf_names)
+        newick = _getNewick(node.get_right(), ",%s" % (newick), node.dist, leaf_names)
+        newick = "(%s" % (newick)
+        return newick
+    
+def _mp2newick(mp, treefile = 'mytree'):
+
+    dist_matrix = mp.dist_matrix
+    leaf_names = mp.flist
+    df = mp.df_embedding[['colors','Subtypes']]
+    
+    dists = squareform(dist_matrix)
+    linkage_matrix = linkage(dists, 'complete')
+    tree = to_tree(linkage_matrix, rd=False)
+    newick = getNewick(tree, "", tree.dist, leaf_names = leaf_names)
+    
+    with open(treefile + '.nwk', 'w') as f:
+        f.write(newick)
+    df.to_excel(treefile + '.xlsx')
+    
+        
+def plot_tree(mp, htmlpath = './', htmlname = None):
+    pass
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