guo2010.py

# coding: utf-8

# In[1]:


import numpy as np
import scipy as sp
import pandas as pd
import sys

import matplotlib.pyplot as plt
plt.style.use(["seaborn-darkgrid", "seaborn-colorblind", "seaborn-notebook"])


# In[2]:


raw_df = pd.read_csv("./guo2010Data.txt", header='infer', index_col=0, sep="\t", encoding=sys.getfilesystemencoding())
raw_df = raw_df.transpose()

time_stages = raw_df['Stage'].astype('int')
raw_df = raw_df.drop('Stage',1)

cell_names = raw_df.index.values
gene_names = raw_df.columns.values

raw_df.shape


# In[3]:


from DTFLOW import *


# In[4]:


z = DTFLOW(raw_df,time_stages)
M= z.get_transition_matrix(10)
S = z.get_diffusionRWR(p=0.9)
Y = z.get_Y(slover='svd',dim=2)


# In[5]:


z.plotY(size=(10,10),dims=[0,1],color ='stages')


# In[6]:


root_list = list(np.where(time_stages.values == 1)[0])
dftimes = z.get_dtflow_times(root_list)
np.savetxt("guo2010_dtflow_times.csv",dftimes,delimiter=',')
z.plotY(size=(10,10),dims=[0,1],color ='dftime')


# In[7]:


branch = z.get_branches(Num=112,delta = 0.9) # 1-11 12-112 
z.plotY(size=(10,10),dims= [0,1],color ='branches')