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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