In [25]:

    

import pandas as pd
from bokeh.plotting import figure, output_notebook, show


df = pd.read_csv('/Users/minzhang/Documents/data/P56_dropseq/results/readCountHumanMouseL2.txt'
                , sep = "\t"
                , names=['cellBarcodes', 'humanReads', 'mouseReads'])

df.tail()


    

    
Out[25]:






  

    

      

      
cellBarcodes
      
humanReads
      
mouseReads
    
  
  

    

      
238241
      
TTTTTTTTTCAG
      
1
      
1
    
    

      
238242
      
TTTTTTTTTCTC
      
0
      
1
    
    

      
238243
      
TTTTTTTTTCTT
      
0
      
4
    
    

      
238244
      
TTTTTTTTTTTA
      
2
      
0
    
    

      
238245
      
TTTTTTTTTTTT
      
110
      
45
    
  

In [28]:

    

def base_plot(tools='pan,wheel_zoom,reset'):
    p = figure(
        tools=tools,
        plot_width=900,
        plot_height=600,
        responsive=True,
        x_range=x_range,
        y_range=y_range,
        outline_line_color=None,
        min_border=0,
    )
    p.axis.visible = False
    p.xgrid.grid_line_color = None
    p.ygrid.grid_line_color = None
    return p
    
options = dict(line_color=None, fill_color='blue', size=5)
x_range = (0,5000)
y_range = (0,5000)


    

In [31]:

    

p = base_plot()
p.circle(x=df.humanReads, y=df.mouseReads, **options)
show(p)


    

In [ ]: