MiBiPreT example: Metabolite Data Analysis with Amersfoort data¶

Diagnostic plots for data analysis on microbial biodegredation at the contaminant Amersfoort site.

Author: Alraune Zech

Data based on the PhD thesis of Johan van Leeuwen, 2021 'Biodegredation of mono- and polyaromatic hydrocarbons in a contaminated aquifer originating from a former Pintsch gas factory site' which is equivalent to the manuscript of van Leeuwen et al., 2022 'Anaerobic degradation of benzene and other aromatic hydrocarbons in a tar-derived plume: Nitrate versus iron reducing conditions', J. of Cont. Hydrol. The data was provided by Johan van Leeuwen.

Background: Amersfoort contaminant site¶

Close to the train station in Amersfoort, the Netherlands, the subsurface is contaminated with organic hydrocarbons forming a NAPL. Contamination originates from decades of operating manufactured gas plant, which dumped tar by-products in waste lagoons. The tar is a DNAPL and has spread into the underlying shallow unconfined aquifer. Sample wells were installed to measure various characteristics of the subsurface. The raw data contains measurements on

• environmental conditions, such as pH, redox potential, concentrations of oxygen, nitrate, etc
• contaminant concentration such as BTEX, indene, indane, naphtalene and multiple other (typically cyclic) petroleum hydrocarbons
• metabolite concentration, i.e. byproducts of degredation processes of contaminant
• isotope measurments for specific contaminants and samples
• counts of genes (RNA/DNA) of mibrobiota that is know to perform biodegredation as well as functional enzymes know to be responsible for biodegredation

Required packages

In [1]:

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd

import matplotlib.pyplot as plt import numpy as np import pandas as pd

In [2]:

import mibiscreen as mbs

import mibiscreen as mbs

Data loading¶

In [3]:

file_path = './amersfoort.xlsx'

file_path = './amersfoort.xlsx'

Load and standardize data of metabolites

Note: Column names of metabolites is not checked. All columns provided (except settings) will be interpreted as individual metabolites.

In [4]:

metabolites_raw,units = mbs.load_excel(file_path,
                                       sheet_name = 'metabolites',
                                       verbose = False)

metabolites,units = mbs.standardize(metabolites_raw,
                                    reduce = False,
                                    verbose=False)

# metabolites_columns = mbs.check_columns(metabolites_raw,verbose = False)
# metabolites_units_check = mbs.check_units(metabolites_raw,verbose = False)
# metabolites_pure = mbs.check_values(metabolites_raw,verbose = False)

#display(metabolites)

metabolites_raw,units = mbs.load_excel(file_path, sheet_name = 'metabolites', verbose = False) metabolites,units = mbs.standardize(metabolites_raw, reduce = False, verbose=False) # metabolites_columns = mbs.check_columns(metabolites_raw,verbose = False) # metabolites_units_check = mbs.check_units(metabolites_raw,verbose = False) # metabolites_pure = mbs.check_values(metabolites_raw,verbose = False) #display(metabolites)

WARNING: Looks like duplicate column names detected.
         They were automatically renamed by pandas into:
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 1.1'
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 2.1'
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 3.1'
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 4.1'
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 5.1'
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 6.1'
 - 'Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 7.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 1.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 2.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 3.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 4.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 5.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 6.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 7.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 8.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 9.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 10.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 11.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 12.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 13.1'
 - 'Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 14.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 1.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 2.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 3.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 4.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 5.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 6.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 7.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 8.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 9.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 10.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 11.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 12.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 13.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 14.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 15.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 16.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 17.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 18.1'
 - 'Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 19.1'
 - 'Octahydro-2-naphthoic acid or Hexahydromethyl indenoic acid.1'
 - 'Indenediol or styrene carboxylic acid - isomer 1.1'
 - 'Indenediol or styrene carboxylic acid - isomer 2.1'
 - 'Indenediol or styrene carboxylic acid - isomer 3.1'
 - 'Indenediol or styrene carboxylic acid - isomer 4.1'
 - 'Indenediol or styrene carboxylic acid - isomer 5.1'
 - 'Indenediol or styrene carboxylic acid - isomer 6.1'
 - 'Indenediol or styrene carboxylic acid - isomer 7.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 1.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 1.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 2.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 2.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 3.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 3.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 4.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 4.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 5.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 5.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 6.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 6.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 7.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 7.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 8.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 8.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 9.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 9.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 10.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 10.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 11.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 11.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 12.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 12.2'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 13.1'
 - 'Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 13.2'
 - 'Dimethyl-benzoic acid or Benzylacetate - isomer 1.1'
 - 'Dimethyl-benzoic acid or Benzylacetate - isomer 2.1'
 - 'Dimethyl-benzoic acid or Benzylacetate - isomer 3.1'
 - 'Dimethyl-benzoic acid or Benzylacetate - isomer 4.1'
 - 'Dimethyl-benzoic acid or Benzylacetate - isomer 5.1'
 - 'Succinic acid or 2-formyl-2-hydroxy-propionate - isomer 1 .1'
 - 'Succinic acid or 2-formyl-2-hydroxy-propionate - isomer 2.1'
 - 'Methyl benzoic acid or Acetylphenol - isomer 1.1'
 - 'Methyl benzoic acid or Acetylphenol - isomer 2.1'
 - 'Methyl benzoic acid or Acetylphenol - isomer 3.1'
 - 'Methyl benzoic acid or Acetylphenol - isomer 4.1'
 - 'Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 1.1'
 - 'Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 2.1'
 - 'Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 3.1'
 - 'Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 4.1'
 - 'Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 5.1'
 - 'Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 6.1'
Duplicate column names will not be identified as standard names.
Consider renaming them.
------------------------------------------------------------------

Metabolites Concentration Analysis¶

Calculating total concentration and counts of metabolites per sample¶

In [5]:

metabolites_total = mbs.total_concentration(metabolites,
                                            name_list = 'all',
                                            include_as = False,    
                                            # verbose = True
                                            )

metabolites_total = mbs.total_concentration(metabolites, name_list = 'all', include_as = False, # verbose = True )

Note that calculated values are not included to data frame as for further analysis all column (except settings) will be used. If including the total concentration, the value of total count will be overestimated by 1.

In [6]:

metabolites_count = mbs.total_count(metabolites,
                                    name_list = 'all', 
                                    include_as = False,    
                                    #verbose = True
                                    )

metabolites_count = mbs.total_count(metabolites, name_list = 'all', include_as = False, #verbose = True )

Previous two steps are equivalent to:

In [7]:

mbs.total_metabolites_concentration(metabolites,
                                    include = True,
                                    verbose = False)

mbs.total_metabolites_concentration(metabolites, include = True, verbose = False)

/opt/hostedtoolcache/Python/3.13.14/x64/lib/python3.13/site-packages/mibiscreen/analysis/sample/concentrations.py:78: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  data[include_as] = tot_conc

Out[7]:

1      39.0
2      58.0
3      29.9
4      38.4
5     123.0
6     374.3
7     142.7
8     655.4
9      57.7
10     61.2
11     41.4
12     36.2
13     51.9
14     87.9
15    110.6
16     48.3
17    156.2
18    140.8
19     76.0
20    124.0
21    104.2
22     87.5
23     53.9
24     50.9
25     50.9
26     32.5
27     68.5
28    106.2
29     33.7
30     51.9
31     50.9
32     48.9
dtype: float64

Now including results as own data column to data frame of metabolites:

In [8]:

print("Names of last two columns", metabolites.columns[-2:].values)

print("Names of last two columns", metabolites.columns[-2:].values)

Names of last two columns <StringArray>
['Phenylbutyrate - isomer 1', 'metabolites_concentration']
Length: 2, dtype: str

In [9]:

mbs.total_metabolites_count(metabolites.iloc[:,:-1],
                            include = True,
                            verbose = False)

mbs.total_metabolites_count(metabolites.iloc[:,:-1], include = True, verbose = False)

/opt/hostedtoolcache/Python/3.13.14/x64/lib/python3.13/site-packages/mibiscreen/analysis/sample/concentrations.py:248: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  data[include_as] = total_count

Out[9]:

1      25
2      28
3      36
4      42
5      83
6     157
7     119
8     172
9      66
10     66
11     16
12     29
13     46
14     78
15    107
16     42
17    111
18     99
19     55
20    133
21    126
22     72
23     48
24     52
25     33
26     16
27     55
28     96
29     17
30     20
31     21
32     17
dtype: int64

In [10]:

print("Names of last two columns", metabolites.columns[-2:].values)

print("Names of last two columns", metabolites.columns[-2:].values)

Names of last two columns <StringArray>
['Phenylbutyrate - isomer 1', 'metabolites_concentration']
Length: 2, dtype: str

In [11]:

display(metabolites_total)

display(metabolites_total)

1      39.0
2      58.0
3      29.9
4      38.4
5     123.0
6     374.3
7     142.7
8     655.4
9      57.7
10     61.2
11     41.4
12     36.2
13     51.9
14     87.9
15    110.6
16     48.3
17    156.2
18    140.8
19     76.0
20    124.0
21    104.2
22     87.5
23     53.9
24     50.9
25     50.9
26     32.5
27     68.5
28    106.2
29     33.7
30     51.9
31     50.9
32     48.9
dtype: float64

In [12]:

mbs.total_metabolites_count(metabolites,
                            include = True,
                            verbose = True)

mbs.total_metabolites_count(metabolites, include = True, verbose = True)

==============================================================
 Running function 'total_metabolites_count()' on data
==============================================================
==============================================================
 Running function 'total_count()' on data
==============================================================
Selecting all data columns except for those with settings.
Selected set of quantities: 
---------------------------
Myristate
4-Hydroxyphenylpyruvate - isomer 2
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 9
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 6
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 11.1
Methylbenzylsuccinic acid - isomer 4
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 2.2
Benzylsuccinic acid
2-naphthoic acid
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 12.2
Dihydro-2-indenoic acid - isomer 3
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 6.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 4
Methyl benzoic acid or Acetylphenol - isomer 2.1
Acenaphthenoic acid - isomer 4
Acenaphthyl methylsuccinate - isomer 1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 5.1
2,3-dihydroxynaphthalene
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 6.1
Dimethyl-naphthoic acid - isomer 8
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 11.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 3
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 2.1
C10H18O5 - isomer 1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 3.2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 3.1
3-naphthalenedicarboxylic acid - isomer 4
Methyl benzoic acid or Acetylphenol - isomer 2
C10H18O5 - isomer 2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 11
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 2
Succinic acid or 2-formyl-2-hydroxy-propionate - isomer 1 .1
Homophthalonitrile
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 4
Hippurate - isomer 3
Dimethyl-naphthoic acid - isomer 2
Indenediol or styrene carboxylic acid - isomer 4
Acenaphthylenoic acid - isomer 4
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 19.1
2-(1-methylhexadecyl)succinate or 2-(2-methylheptadecyl)malonate
2-hydroxy-2-methyl-malonate
Methylglyoxal
Quinolinic acid - isomer 1
Benzylsuccinic acid - isomer 1
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 7
Ethylmalonate - isomer 1
3-o-toluoyl propionic acid - isomer 2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 4.1
2-HIBA or hydroxy butyrate - isomer 3
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 2.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 8
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 3
2-HIBA or hydroxy butyrate - isomer 1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 17.1
2-isopropylmalic acid - isomer 2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 7.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 7.2
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 9.1
4-Hydroxyphenylpyruvate - isomer 1
Adipic acid
3-o-toluoyl propionic acid - isomer 3
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 9
Octanoate - isomer 1
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 3.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 9.1
3-o-toluoyl propionic acid - isomer 5
Dihydro-2-indenoic acid - isomer 1
3-naphthalenedicarboxylic acid - isomer 1
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 3.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 13.2
Fluorene-carboxylic acid - isomer 6
4-hydroxy benzoic acid
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 11
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 8.1
Hippurate - isomer 5
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 14
P-cresol - isomer 4
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 8
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 6.1
Dimethyl-naphthoic acid - isomer 11
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 6.1
Succinic acid or 2-formyl-2-hydroxy-propionate - isomer 1 
Methyl benzoic acid or Acetylphenol - isomer 1.1
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 4.1
3-o-toluoyl propionic acid - isomer 10
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 13.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 5
Cinnamic acid
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 4.1
Indenediol or styrene carboxylic acid - isomer 7.1
Octahydro-2-naphthoic acid or Hexahydromethyl indenoic acid
3-o-toluoyl propionic acid - isomer 14
Indenediol or styrene carboxylic acid - isomer 6
Fumaric acid - isomer 2
Acenaphthylenoic acid - isomer 2
Butylmalonate - isomer 4
3-o-toluoyl propionic acid - isomer 16
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 12.1
T-butyl formate
Indenediol or styrene carboxylic acid - isomer 3.1
Benzoylacetic acid
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 18.1
Indenediol or styrene carboxylic acid - isomer 5
Dimethyl-benzoic acid or Benzylacetate - isomer 4
Butylmalonate - isomer 3
Dicyclononane-2-carboxylate (octahydro-2-indenoic acid)
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 6
Acenaphthenoic acid - isomer 2
2-methylindene - isomer 3
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 1
Indenediol or styrene carboxylic acid - isomer 3
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 1
Valeric acid
Hippurate - isomer 6
3-o-toluoyl propionic acid - isomer 4
P-cresol - isomer 3
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 15.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 1.2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 6.2
phenol
Nonanoate - isomer 2
Indenediol or styrene carboxylic acid - isomer 6.1
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 10
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 5.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 1.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 12.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 10.1
Fluorene-carboxylic acid - isomer 7
Trimethylbenzoic acid - isomer 1
Nonanoate - isomer 1
Succinic acid or 2-formyl-2-hydroxy-propionate - isomer 2
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 11
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 18
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 16
2-(1-methyldodecyl)succinate or 2-(2-methyltridecyl)malonate - isomer 2
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 5
Phenanthroic acid - isomer 1
3-OH-isovaleric acid - isomer 4
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 16.1
4-aminobenzoic acid
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 9
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 14.1
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 5
2,3-dihydroxy-2-methylpropionate
Indenediol or styrene carboxylic acid - isomer 1.1
Acenaphthyl methylsuccinate - isomer 2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 10.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 10
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 2.1
3-OH-isovaleric acid - isomer 2
Acenaphthenoic acid - isomer 1
Dimethyl-naphthoic acid - isomer 9
Indyl methyl succinic acid - isomer 2
Phenylbutyrate - isomer 1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 1.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 12
Dimethyl-naphthoic acid - isomer 3
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 6.1
Laurate
Dimethyl-benzoic acid or Benzylacetate - isomer 1
3-OH-isovaleric acid - isomer 1
3-o-toluoyl propionic acid - isomer 13
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 4.2
3-o-toluoyl propionic acid - isomer 12
3-naphthalenedicarboxylic acid - isomer 6
Dimethyl-benzoic acid or Benzylacetate - isomer 2.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 5.1
Benzoic acid
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 2.1
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 2
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 4.1
Acenaphthenoic acid - isomer 5
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 7
Indenediol or styrene carboxylic acid - isomer 2.1
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 1.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 2
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 5
Methyl benzoic acid or Acetylphenol - isomer 4
Hydroxycaproate
Indenediol - isomer 1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 5.2
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 3
Dimethyl-benzoic acid or Benzylacetate - isomer 5.1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 7
P-cresol - isomer 1
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 7
Hexahydro-2-indenoic acid - isomer 2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 11.2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 7
3-o-toluoyl propionic acid - isomer 6
3-o-toluoyl propionic acid - isomer 1
Dimethyl-naphthoic acid - isomer 10
Indenediol or styrene carboxylic acid - isomer 7
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 1
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 3
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 10
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 6
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 9.1
3-o-toluoyl propionic acid - isomer 8
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 10.1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 8.2
Indyl methyl succinic acid - isomer 1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 19
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 1.1
Fluorene-carboxylic acid - isomer 1
3-o-toluoyl propionic acid - isomer 15
Dihydro-2-indenoic acid - isomer 5
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 13
Naphthyl-2-methyl-succinate - isomer 2
P-cresol - isomer 2
Dihydro-2-indenoic acid - isomer 4
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 14
Dimethyl-naphthoic acid - isomer 1
Dimethyl-naphthoic acid - isomer 5
Hippurate - isomer 2
Fluorene-carboxylic acid - isomer 4
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 3
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 1
Benzylsuccinic acid - isomer 4
Acenaphthylenoic acid - isomer 3
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 12
Ethylmalonate - isomer 2
2-carboxycyclohexylacetic acid 
Dimethyl-benzoic acid or Benzylacetate - isomer 4.1
Dimethyl-benzoic acid or Benzylacetate - isomer 3
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 5
3-o-toluoyl propionic acid - isomer 7
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 2.1
Octanoate - isomer 2
Fluorene-carboxylic acid - isomer 5
Indenediol or styrene carboxylic acid - isomer 4.1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 17
Indenediol or styrene carboxylic acid - isomer 5.1
metabolites_concentration
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 9
Butylmalonate - isomer 1
Octahydro-2-naphthoic acid or Hexahydromethyl indenoic acid.1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 4.1
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 6
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 5.1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 11.1
Tryptophan - isomer 2
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 7.1
Methylbenzylsuccinic acid - isomer 1
1H-indene-2-carboxylic acid - isomer 2
2-ethylhexanol
Dimethyl-benzoic acid or Benzylacetate - isomer 1.1
Ethylmalonate - isomer 3
Dimethyl-naphthoic acid - isomer 4
Hydroxy-naphthoic acid
2-(1-methyltetradecyl)succinate or 2-(2-methylpentadecyl)malonate - isomer 2
Acenaphthenoic acid - isomer 3
Methyl benzoic acid or Acetylphenol - isomer 3.1
Methylmalonate semialdehyde
Quinolinic acid - isomer 2
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 3
Dimethyl-naphthoic acid - isomer 7
Methyl benzoic acid or Acetylphenol - isomer 4.1
Dimethyl-benzoic acid or Benzylacetate - isomer 2
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 2
Fumaric acid - isomer 1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 4
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 2
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 5.1
3-naphthalenedicarboxylic acid - isomer 2
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 8.1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 12
3-naphthalenedicarboxylic acid - isomer 3
Methyl benzoic acid or Acetylphenol - isomer 1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 1
Methyl benzoic acid or Acetylphenol - isomer 3
Methylbenzylsuccinic acid - isomer 3
Phenylsuccinic acid - isomer 1
Indenediol or styrene carboxylic acid - isomer 1
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 8
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 13
Acenaphthylenoic acid - isomer 1
Phenylglyoxylic acid
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 8
Phenanthroic acid - isomer 4
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 13
Tryptophan - isomer 1
2-isopropylmalic acid - isomer 1
Dimethyl-benzoic acid or Benzylacetate - isomer 3.1
2-methyl 2-hydroxy-propanal
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 5
Benzylsuccinic acid - isomer 3
Indenediol or styrene carboxylic acid - isomer 2
Butylmalonate - isomer 2
Naphthyl-2-methyl-succinate - isomer 1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 7.1
Benzylsuccinic acid - isomer 2
3-nonenoate
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 13.1
Fluorene-carboxylic acid - isomer 2
2-(1-methyltetradecyl)succinate or 2-(2-methylpentadecyl)malonate - isomer 1
Methylbenzylsuccinic acid - isomer 2
Hydroxyphenylacetic acid
2-HIBA or hydroxy butyrate - isomer 2
1-naphthoic acid
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 8.1
Hippurate - isomer 7
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 2
Butyrate
Dihydro-2-indenoic acid - isomer 2
Dimethyl-benzoic acid or Benzylacetate - isomer 5
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 6
Hippurate - isomer 1
Phenanthroic acid - isomer 2
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 14.1
Phenylsuccinic acid - isomer 2
2-carboxycyclohexylacetic acid
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 4
Hexahydro-2-indenoic acid - isomer 1
3-naphthalenedicarboxylic acid - isomer 5
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 1.1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 3.1
2-(1-methyldodecyl)succinate or 2-(2-methyltridecyl)malonate - isomer 1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 9.2
3-o-toluoyl propionic acid - isomer 11
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 7.1
Fluorene-carboxylic acid - isomer 3
Succinic acid or 2-formyl-2-hydroxy-propionate - isomer 2.1
Hippurate - isomer 4
2-methylindene - isomer 1
Dihydro-2-indenoic acid - isomer 6
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 10
Benzoylacetic acid, P-coumaric acid or Hydroxycinnamate - isomer 4
3-o-toluoyl propionic acid - isomer 17
Carboxylated methyl indene or Dihydro-naphthoic acid - isomer 4
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 15
3-o-toluoyl propionic acid - isomer 9
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 12.1
1H-indene-2-carboxylic acid - isomer 1
Tetrahydro-2-indenoic acid, Phenylbutyrate or Trimethylbenzoic acid - isomer 10.2
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 3.1
2-methylindene - isomer 2
Naphthaleneacetic acid or methyl-naphthoic acid - isomer 1
Nicotinic acid
Acetylphenol - isomer 1
Dihydromethyl indenoic acid, Tetrahydro-naphthoic acid or 2,3-dihydro-1H-indene-acetic acid - isomer 6
Phenanthroic acid - isomer 3
Dimethyl-naphthoic acid - isomer 6
Tetrahydromethyl indenoic acid or Hexahydro-naphthoic acid - isomer 13.1
Decahydro-naphthoic acid
1H-indene-2-carboxylic acid
Phenylsuccinic acid - isomer 3
Methylbenzylsuccinic acid - isomer 5
3-OH-isovaleric acid - isomer 3
_____________________________________________________________
________________________________________________________________
Number of quantities out of 349 exceeding               concentration of 0.00 ug/l :
1      26
2      29
3      37
4      43
5      84
6     158
7     120
8     173
9      67
10     67
11     17
12     30
13     47
14     79
15    108
16     43
17    112
18    100
19     56
20    134
21    127
22     73
23     49
24     53
25     34
26     17
27     56
28     97
29     18
30     21
31     22
32     18
dtype: int64
--------------------------------------------------
Series saved as column 'metabolites_count' within provided DataFrame
---------------------------------------------------------------------------

/opt/hostedtoolcache/Python/3.13.14/x64/lib/python3.13/site-packages/mibiscreen/analysis/sample/concentrations.py:248: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  data[include_as] = total_count

Out[12]:

1      26
2      29
3      37
4      43
5      84
6     158
7     120
8     173
9      67
10     67
11     17
12     30
13     47
14     79
15    108
16     43
17    112
18    100
19     56
20    134
21    127
22     73
23     49
24     53
25     34
26     17
27     56
28     97
29     18
30     21
31     22
32     18
dtype: int64

Plotting total concentration of metabolites¶

In [13]:

mbs.contaminants_bar(metabolites,
                     list_contaminants = ['metabolites_concentration'],
                     list_labels = ['all metabolites'],
                     figsize = [18,5],
                     textsize = 14,
                     ylabel = r'Total metabolites concentration [$\mu$g/l]',
                     loc='upper left',
                     title_text = 'Total concentration of metabolites per sample',
                     )

mbs.contaminants_bar(metabolites, list_contaminants = ['metabolites_concentration'], list_labels = ['all metabolites'], figsize = [18,5], textsize = 14, ylabel = r'Total metabolites concentration [$\mu$g/l]', loc='upper left', title_text = 'Total concentration of metabolites per sample', )

Out[13]:

(<Figure size 1800x500 with 1 Axes>,
 <Axes: title={'center': 'Total concentration of metabolites per sample'}, xlabel='Samples', ylabel='Total metabolites concentration [$\\mu$g/l]'>)

Producing the plot individually using matplotlib and numpy for individual adaptions:

In [14]:

plt.figure(figsize = [18,5])
plt.bar(np.arange(len(metabolites_total.values)),metabolites_total.values,label='all')
plt.xlabel('Samples')
plt.ylabel(r'Total metabolites concentration [$\mu$g/l]')
plt.title('Total concentration of metabolites per sample')

plt.figure(figsize = [18,5]) plt.bar(np.arange(len(metabolites_total.values)),metabolites_total.values,label='all') plt.xlabel('Samples') plt.ylabel(r'Total metabolites concentration [$\mu$g/l]') plt.title('Total concentration of metabolites per sample')

Out[14]:

Text(0.5, 1.0, 'Total concentration of metabolites per sample')

Plot with sorting of values and sample names

In [15]:

mbs.contaminants_bar(metabolites,
                     list_contaminants = ['metabolites_concentration'],
                     list_labels = ['all metabolites'],
                     sort = True,
                     name_sample = True,
                     figsize = [18,5],
                     textsize = 12,
                     ylabel = r'Total metabolites concentration [$\mu$g/l]',
                     loc='upper left',
                     title_text = 'Total concentration of metabolites per sample',
                     xtick_autorotate = True,
                      # save_fig = 'metabolites_bar.png',
                     )

mbs.contaminants_bar(metabolites, list_contaminants = ['metabolites_concentration'], list_labels = ['all metabolites'], sort = True, name_sample = True, figsize = [18,5], textsize = 12, ylabel = r'Total metabolites concentration [$\mu$g/l]', loc='upper left', title_text = 'Total concentration of metabolites per sample', xtick_autorotate = True, # save_fig = 'metabolites_bar.png', )

Out[15]:

(<Figure size 1800x500 with 1 Axes>,
 <Axes: title={'center': 'Total concentration of metabolites per sample'}, xlabel='Samples', ylabel='Total metabolites concentration [$\\mu$g/l]'>)

Producing the plot individually using matplotlib and numpy for individual adaptions:

In [16]:

fig = plt.figure(figsize = [18,5])
sort_args = np.argsort(metabolites['metabolites_concentration'].values)
plt.bar(metabolites.sample_nr.values[sort_args],metabolites['metabolites_concentration'].values[sort_args],label='all')
plt.xlabel('Samples')
plt.ylabel(r'Total metabolites concentration [$\mu$g/l]')
plt.title('Total concentration of metabolites per sample')
fig.autofmt_xdate(bottom=0.2, rotation=30, ha='right', which='major')

fig = plt.figure(figsize = [18,5]) sort_args = np.argsort(metabolites['metabolites_concentration'].values) plt.bar(metabolites.sample_nr.values[sort_args],metabolites['metabolites_concentration'].values[sort_args],label='all') plt.xlabel('Samples') plt.ylabel(r'Total metabolites concentration [$\mu$g/l]') plt.title('Total concentration of metabolites per sample') fig.autofmt_xdate(bottom=0.2, rotation=30, ha='right', which='major')

Plotting total counts of metabolites¶

In [17]:

mbs.contaminants_bar(metabolites,
                     list_contaminants = ['metabolites_count'],
                     list_labels = ['total metabolites count'],
                     sort = True,
                     name_sample = True,
                     figsize = [18,5],
                     textsize = 12,
                     ylabel = r'Total metabolites count',
                     loc='upper left',
                     title_text = 'Total count of metabolites per sample',
                     xtick_autorotate = True,
                      # save_fig = 'metabolites_count_bar.png',
                     )

mbs.contaminants_bar(metabolites, list_contaminants = ['metabolites_count'], list_labels = ['total metabolites count'], sort = True, name_sample = True, figsize = [18,5], textsize = 12, ylabel = r'Total metabolites count', loc='upper left', title_text = 'Total count of metabolites per sample', xtick_autorotate = True, # save_fig = 'metabolites_count_bar.png', )

Out[17]:

(<Figure size 1800x500 with 1 Axes>,
 <Axes: title={'center': 'Total count of metabolites per sample'}, xlabel='Samples', ylabel='Total metabolites count'>)

Relating Metabolite activity to electron availability¶

Load data of contaminants and geochemicals to identify electron availability and NA activity color¶

In [18]:

contaminants_raw,_ = mbs.load_excel(file_path,
                                    sheet_name = 'contaminants',
                                    verbose = False)
contaminants,units = mbs.standardize(contaminants_raw,verbose = False)
environment_raw,_ = mbs.load_excel(file_path,
                                   sheet_name = 'environment',
                                   verbose = False)
environment,units = mbs.standardize(environment_raw,verbose = False)

contaminants_raw,_ = mbs.load_excel(file_path, sheet_name = 'contaminants', verbose = False) contaminants,units = mbs.standardize(contaminants_raw,verbose = False) environment_raw,_ = mbs.load_excel(file_path, sheet_name = 'environment', verbose = False) environment,units = mbs.standardize(environment_raw,verbose = False)

Enrich data by data analysis needed¶

In [19]:

mbs.total_contaminant_concentration(contaminants,include = True)
mbs.total_metabolites_count(metabolites,include = True)
data_NA = mbs.merge_data([environment,contaminants,metabolites])
mbs.sample_NA_traffic(data_NA,include = True)

mbs.total_contaminant_concentration(contaminants,include = True) mbs.total_metabolites_count(metabolites,include = True) data_NA = mbs.merge_data([environment,contaminants,metabolites]) mbs.sample_NA_traffic(data_NA,include = True)

WARNING: There are quantities from name list not in data
Maybe data not in standardized format. Run 'standardize()' first.
_________________________________________________________________
WARNING: There are quantities from name list not in data
Maybe data not in standardized format. Run 'standardize()' first.
_________________________________________________________________

/opt/hostedtoolcache/Python/3.13.14/x64/lib/python3.13/site-packages/mibiscreen/analysis/sample/screening_NA.py:274: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  data[names.name_na_traffic_light] = NA_traffic

Out[19]:

0     green
1     green
2     green
3     green
4     green
5     green
6     green
7     green
8     green
9     green
10    green
11      red
12      red
13      red
14      red
15    green
16      red
17      red
18    green
19    green
20    green
21      red
22    green
23      red
24      red
25      red
26      red
27      red
28      red
29      red
30      red
31    green
32    green
Name: na_traffic_light, dtype: str

Activity plot linking contaminant concentration to metabolite occurence and NA screening¶

In [20]:

data_activity =  mbs.activity_data_prep(data_NA)
data_activity['tot_cont'] = data_activity['tot_cont']*0.001

data_activity = mbs.activity_data_prep(data_NA) data_activity['tot_cont'] = data_activity['tot_cont']*0.001

In [21]:

#fig, ax = mbs.activity_plot(data_activity)
fig, ax = mbs.activity_plot(data_activity,
                       figsize = [6,4],
                       textsize = 12,
                       xscale = 'log',
                       markersize = 60,
                       loc='center right',
                       xlabel = r"Concentration contaminants [mg/L]",
                       #save_fig = 'activity.png'
                       )

#fig, ax = mbs.activity_plot(data_activity) fig, ax = mbs.activity_plot(data_activity, figsize = [6,4], textsize = 12, xscale = 'log', markersize = 60, loc='center right', xlabel = r"Concentration contaminants [mg/L]", #save_fig = 'activity.png' )