TimeVis Plugin System Demonstration

Authors: Ce Gao

Created: 2015-05-27

0. Some preparation



In [1]:

    
%matplotlib inline

1. import package



In [2]:

    
import os
os.chdir('../')
import timevis
from timevis.plugin import Plugin

2. Create a customized plugin classes inheritting Plugin base class



In [3]:

    
class Ext_1(Plugin): pass
class Ext_2(Plugin): pass

3. Interactive use of timevis

0) Initiate an object



In [4]:

    
p1 = Ext_1()

1) Get Experiment table



In [5]:

    
p1.experiment.head()

2) Get Layout table

The rows are sorted by well column



In [8]:

    
p1.layout.sort('well').head()

3) Get Plate table

The rows are sorted by well, channel and time columns



In [10]:

    
p1.plate.sort(['well', 'channel', 'time']).head()

4) Plot time series data for a certain well on the microplate



In [11]:

    
p1.plate[p1.plate.well == 'A01'].plot(x='time', y='measure')









    Out[11]:





<matplotlib.axes._subplots.AxesSubplot at 0x7f47040798d0>

5) Plot value distribution for the plate



In [13]:

    
p1.plate.measure.plot(subplots=True, kind='hist')









    Out[13]:





array([<matplotlib.axes._subplots.AxesSubplot object at 0x7f4703e459d0>], dtype=object)

6) Summarize the number of time points for each well



In [15]:

    
p1.plate.groupby('well').measure.size().head()









    Out[15]:





well
A01    4
A02    4
A03    4
A04    4
A05    4
dtype: int64

4. Plugin detection

The customize plugin classes will be registered and used by TimeVis



In [16]:

    
timevis.plugin.plugins









    Out[16]:





{'Ext_1': __main__.Ext_1, 'Ext_2': __main__.Ext_2}



In [ ]:

	eid	lid	fid	pid	layout	factor	well	level
91	1	1	1	1	Layout 1	Doses	A01	42
187	1	1	2	1	Layout 1	Genes	A01	bb
89	1	1	1	1	Layout 1	Doses	A02	42
185	1	1	2	1	Layout 1	Genes	A02	bb
90	1	1	1	1	Layout 1	Doses	A03	42

	pid	cid	channel	well	time	measure
0	1	1	GFP	A01	00:00:00	3.496714
96	1	1	GFP	A01	00:05:00	4.592241
192	1	1	GFP	A01	00:10:00	5.428187
288	1	1	GFP	A01	00:15:00	6.842976
1	1	1	GFP	A02	00:00:00	2.861736