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In [1]:

    
import matplotlib as mpl
mpl.use('TkAgg')
import matplotlib.pyplot as plt
%matplotlib inline

import pandas as pd
import seaborn as sns



In [2]:

    
gene_data = pd.read_csv('summary.dat', sep = '\t')



In [3]:

    
gene_data.head()









    Out[3]:






  
    
      
      genome
      locus_tag
      product
      LakWasM100_LOW12_2_rpkm
      LakWasMe97_LOW12_2_rpkm
      LakWasMe98_LOW12_2_rpkm
      LakWasMe99_LOW12_2_rpkm
      LakWasM104_HOW12_2_rpkm
      LakWasM105_HOW12_2_rpkm
      LakWasM106_HOW12_2_rpkm
      ...
      LakWasMet56_HOW8_2_rpkm
      LakWasMet57_HOW8_2_rpkm
      LakWasMet58_HOW8_2_rpkm
      LakWasMet61_LOW9_2_rpkm
      LakWasMet62_LOW9_2_rpkm
      LakWasMet63_LOW9_2_rpkm
      LakWasMet64_LOW9_2_rpkm
      LakWasMet67_HOW9_2_rpkm
      LakWasMet69_HOW9_2_rpkm
      LakWasMet70_HOW9_2_rpkm
    
  
  
    
      0
      Acidovora-69x (UID4105)
      Ga0081644_10011
      serine/threonine protein kinase
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
    
    
      1
      Acidovora-69x (UID4105)
      Ga0081644_10012
      simple sugar transport system permease protein
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
    
    
      2
      Acidovora-69x (UID4105)
      Ga0081644_10013
      nucleoside ABC transporter ATP-binding protein
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      1
      0
      0
      0
      0
      1
      0
      0
    
    
      3
      Acidovora-69x (UID4105)
      Ga0081644_10021
      hypothetical protein
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
    
    
      4
      Acidovora-69x (UID4105)
      Ga0081644_10022
      D-amino-acid dehydrogenase
      0
      0
      0
      0
      0
      1
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      2
      0
      2
    
  

5 rows × 86 columns



In [4]:

    
gene_data.set_index(['genome', 'locus_tag', 'product'], inplace=True)



In [5]:

    
gene_data.head()









    Out[5]:






  
    
      
      
      
      LakWasM100_LOW12_2_rpkm
      LakWasMe97_LOW12_2_rpkm
      LakWasMe98_LOW12_2_rpkm
      LakWasMe99_LOW12_2_rpkm
      LakWasM104_HOW12_2_rpkm
      LakWasM105_HOW12_2_rpkm
      LakWasM106_HOW12_2_rpkm
      LakWasM109_LOW13_2_rpkm
      LakWasM110_LOW13_2_rpkm
      LakWasM111_LOW13_2_rpkm
      ...
      LakWasMet56_HOW8_2_rpkm
      LakWasMet57_HOW8_2_rpkm
      LakWasMet58_HOW8_2_rpkm
      LakWasMet61_LOW9_2_rpkm
      LakWasMet62_LOW9_2_rpkm
      LakWasMet63_LOW9_2_rpkm
      LakWasMet64_LOW9_2_rpkm
      LakWasMet67_HOW9_2_rpkm
      LakWasMet69_HOW9_2_rpkm
      LakWasMet70_HOW9_2_rpkm
    
    
      genome
      locus_tag
      product
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      Acidovora-69x (UID4105)
      Ga0081644_10011
      serine/threonine protein kinase
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
    
    
      Ga0081644_10012
      simple sugar transport system permease protein
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
    
    
      Ga0081644_10013
      nucleoside ABC transporter ATP-binding protein
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      1
      0
      0
      0
      0
      1
      0
      0
    
    
      Ga0081644_10021
      hypothetical protein
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      0
      0
      0
    
    
      Ga0081644_10022
      D-amino-acid dehydrogenase
      0
      0
      0
      0
      0
      1
      0
      0
      0
      0
      ...
      0
      0
      0
      0
      0
      0
      0
      2
      0
      2
    
  

5 rows × 83 columns



In [6]:

    
sample_sums = pd.DataFrame({'read counts':gene_data.sum(index=0)})



In [7]:

    
sample_sums.head()









    Out[7]:






  
    
      
      read counts
    
  
  
    
      LakWasM100_LOW12_2_rpkm
      1266898
    
    
      LakWasMe97_LOW12_2_rpkm
      1116377
    
    
      LakWasMe98_LOW12_2_rpkm
      1119813
    
    
      LakWasMe99_LOW12_2_rpkm
      1242902
    
    
      LakWasM104_HOW12_2_rpkm
      1269758



In [8]:

    
sample_sums['reads/10^6'] = sample_sums['read counts']/(10**6)



In [ ]:

    
sample_sums[]



In [13]:

    
sample_sums.index









    Out[13]:





Index(['LakWasM100_LOW12_2_rpkm', 'LakWasMe97_LOW12_2_rpkm',
       'LakWasMe98_LOW12_2_rpkm', 'LakWasMe99_LOW12_2_rpkm',
       'LakWasM104_HOW12_2_rpkm', 'LakWasM105_HOW12_2_rpkm',
       'LakWasM106_HOW12_2_rpkm', 'LakWasM109_LOW13_2_rpkm',
       'LakWasM110_LOW13_2_rpkm', 'LakWasM111_LOW13_2_rpkm',
       'LakWasM112_LOW13_2_rpkm', 'LakWasM115_HOW13_2_rpkm',
       'LakWasM116_HOW13_2_rpkm', 'LakWasM117_HOW13_2_rpkm',
       'LakWasM118_HOW13_2_rpkm', 'LakWasM121_LOW14_2_rpkm',
       'LakWasM122_LOW14_2_rpkm', 'LakWasM123_LOW14_2_rpkm',
       'LakWasM124_LOW14_2_rpkm', 'LakWasM127_HOW14_2_rpkm',
       'LakWasM128_HOW14_2_rpkm', 'LakWasM129_HOW14_2_rpkm',
       'LakWasM130_HOW14_2_rpkm', 'LakWasMe73_LOW10_2_rpkm',
       'LakWasMe74_LOW10_2_rpkm', 'LakWasMe75_LOW10_2_rpkm',
       'LakWasMe76_LOW10_2_rpkm', 'LakWasMe79_HOW10_2_rpkm',
       'LakWasMe80_HOW10_2_rpkm', 'LakWasMe81_HOW10_2_rpkm',
       'LakWasMe82_HOW10_2_rpkm', 'LakWasMe85_LOW11_2_rpkm',
       'LakWasMe86_LOW11_2_rpkm', 'LakWasMe91_HOW11_2_rpkm',
       'LakWasMe92_HOW11_2_rpkm', 'LakWasMe93_HOW11_2_rpkm',
       'LakWasMe94_HOW11_2_rpkm', 'LakWasMeta1_LOW4_2_rpkm',
       'LakWasMeta2_LOW4_2_rpkm', 'LakWasMeta3_LOW4_2_rpkm',
       'LakWasMeta4_LOW4_2_rpkm', 'LakWasMet10_HOW4_2_rpkm',
       'LakWasMeta7_HOW4_2_rpkm', 'LakWasMeta8_HOW4_2_rpkm',
       'LakWasMeta9_HOW4_2_rpkm', 'LakWasMet13_LOW5_2_rpkm',
       'LakWasMet14_LOW5_2_rpkm', 'LakWasMet15_LOW5_2_rpkm',
       'LakWasMet16_LOW5_2_rpkm', 'LakWasMet19_HOW5_2_rpkm',
       'LakWasMet20_HOW5_2_rpkm', 'LakWasMet21_HOW5_2_rpkm',
       'LakWasMet22_HOW5_2_rpkm', 'LakWasMet25_LOW6_2_rpkm',
       'LakWasMet26_LOW6_2_rpkm', 'LakWasMet27_LOW6_2_rpkm',
       'LakWasMet28_LOW6_2_rpkm', 'LakWasMet31_HOW6_2_rpkm',
       'LakWasMet32_HOW6_2_rpkm', 'LakWasMet33_HOW6_2_rpkm',
       'LakWasMet34_HOW6_2_rpkm', 'LakWasMet37_LOW7_2_rpkm',
       'LakWasMet38_LOW7_2_rpkm', 'LakWasMet39_LOW7_2_rpkm',
       'LakWasMet40_LOW7_2_rpkm', 'LakWasMet43_HOW7_2_rpkm',
       'LakWasMet44_HOW7_2_rpkm', 'LakWasMet45_HOW7_2_rpkm',
       'LakWasMet49_LOW8_2_rpkm', 'LakWasMet50_LOW8_2_rpkm',
       'LakWasMet51_LOW8_2_rpkm', 'LakWasMet52_LOW8_2_rpkm',
       'LakWasMet55_HOW8_2_rpkm', 'LakWasMet56_HOW8_2_rpkm',
       'LakWasMet57_HOW8_2_rpkm', 'LakWasMet58_HOW8_2_rpkm',
       'LakWasMet61_LOW9_2_rpkm', 'LakWasMet62_LOW9_2_rpkm',
       'LakWasMet63_LOW9_2_rpkm', 'LakWasMet64_LOW9_2_rpkm',
       'LakWasMet67_HOW9_2_rpkm', 'LakWasMet69_HOW9_2_rpkm',
       'LakWasMet70_HOW9_2_rpkm'],
      dtype='object')



In [18]:

    
sample_sums.loc['LakWasM106_HOW12_2_rpkm']









    Out[18]:





read counts    1001033.000000
reads/10^6           1.001033
Name: LakWasM106_HOW12_2_rpkm, dtype: float64



In [9]:

    
sample_sums.head()









    Out[9]:






  
    
      
      read counts
      reads/10^6
    
  
  
    
      LakWasM100_LOW12_2_rpkm
      1266898
      1.266898
    
    
      LakWasMe97_LOW12_2_rpkm
      1116377
      1.116377
    
    
      LakWasMe98_LOW12_2_rpkm
      1119813
      1.119813
    
    
      LakWasMe99_LOW12_2_rpkm
      1242902
      1.242902
    
    
      LakWasM104_HOW12_2_rpkm
      1269758
      1.269758



In [10]:

    
ax = sample_sums['reads/10^6'].plot.hist(range=[0, 1.5], bins = 60) #range=[6.5, 12.5])
fig = ax.get_figure()
fig.savefig('reads_per_sample--unnormalized.pdf')



In [11]:

    
gene_sums = pd.DataFrame({'gene sum':gene_data.sum(axis=1, index=2)})



In [ ]:

    
gene_sums['gene sum'] = gene_sums['gene sum'].astype('int')



In [ ]:

    
gene_sums = gene_sums[gene_sums['gene sum'] > 0]

import numpy as np

gene_sums['log10(gene sum)'] = np.log10(gene_sums['gene sum'])



In [ ]:

    
gene_sums.head()



In [ ]:

    
gene_sums.head() #.plot(kind='hist')



In [ ]:

    
gene_sums.shape



In [ ]:

    
fig, ax = plt.subplots()
gene_sums['gene sum'].hist(ax=ax, bins=100, )
ax.set_yscale('log')
ax.set_xlabel('...')



In [ ]:

    
gene_sums[gene_sums['gene sum'] > 5].head()



In [ ]:

    
gene_sums[gene_sums['gene sum'] > 10**6].head()



In [ ]:

    
fig, ax = plt.subplots()
gene_sums[gene_sums['gene sum'] > 0]['gene sum'].hist(ax=ax, bins=100, )
ax.set_yscale('log')
ax.set_xlabel('number of genes with ')



In [ ]:

    
fig, ax = plt.subplots()
gene_sums[gene_sums['gene sum'] > 10**4]['gene sum'].hist(ax=ax, bins=100, )
ax.set_yscale('log')
ax.set_xlabel('number of genes with ')



In [ ]:

	genome	locus_tag	product	LakWasM105_HOW12_2_rpkm	...	LakWasMet58_HOW8_2_rpkm	LakWasMet67_HOW9_2_rpkm	LakWasMet70_HOW9_2_rpkm
0	Acidovora-69x (UID4105)	Ga0081644_10011	serine/threonine protein kinase	0	...	0	0	0
1	Acidovora-69x (UID4105)	Ga0081644_10012	simple sugar transport system permease protein	0	...	0	0	0
2	Acidovora-69x (UID4105)	Ga0081644_10013	nucleoside ABC transporter ATP-binding protein	0	...	1	1	0
3	Acidovora-69x (UID4105)	Ga0081644_10021	hypothetical protein	0	...	0	0	0
4	Acidovora-69x (UID4105)	Ga0081644_10022	D-amino-acid dehydrogenase	1	...	0	2	2

			LakWasM100_LOW12_2_rpkm	LakWasMe97_LOW12_2_rpkm	LakWasMe98_LOW12_2_rpkm	LakWasMe99_LOW12_2_rpkm	LakWasM104_HOW12_2_rpkm	LakWasM105_HOW12_2_rpkm	LakWasM106_HOW12_2_rpkm	LakWasM109_LOW13_2_rpkm	LakWasM110_LOW13_2_rpkm	LakWasM111_LOW13_2_rpkm	...	LakWasMet56_HOW8_2_rpkm	LakWasMet57_HOW8_2_rpkm	LakWasMet58_HOW8_2_rpkm	LakWasMet61_LOW9_2_rpkm	LakWasMet62_LOW9_2_rpkm	LakWasMet63_LOW9_2_rpkm	LakWasMet64_LOW9_2_rpkm	LakWasMet67_HOW9_2_rpkm	LakWasMet69_HOW9_2_rpkm	LakWasMet70_HOW9_2_rpkm
genome	locus_tag	product
Acidovora-69x (UID4105)	Ga0081644_10011	serine/threonine protein kinase	0	0	0	0	0	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	0
	Ga0081644_10012	simple sugar transport system permease protein	0	0	0	0	0	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	0
	Ga0081644_10013	nucleoside ABC transporter ATP-binding protein	0	0	0	0	0	0	0	0	0	0	...	0	0	1	0	0	0	0	1	0	0
	Ga0081644_10021	hypothetical protein	0	0	0	0	0	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	0
	Ga0081644_10022	D-amino-acid dehydrogenase	0	0	0	0	0	1	0	0	0	0	...	0	0	0	0	0	0	0	2	0	2

	read counts
LakWasM100_LOW12_2_rpkm	1266898
LakWasMe97_LOW12_2_rpkm	1116377
LakWasMe98_LOW12_2_rpkm	1119813
LakWasMe99_LOW12_2_rpkm	1242902
LakWasM104_HOW12_2_rpkm	1269758

	read counts	reads/10^6
LakWasM100_LOW12_2_rpkm	1266898	1.266898
LakWasMe97_LOW12_2_rpkm	1116377	1.116377
LakWasMe98_LOW12_2_rpkm	1119813	1.119813
LakWasMe99_LOW12_2_rpkm	1242902	1.242902
LakWasM104_HOW12_2_rpkm	1269758	1.269758