Visualisation of an EnzymeML document#

PyEnzyme offers the ability to visualize experimental data present in an EnzymeML document for inspection and publication. The method can be specified such that either static or interactive visualisations are be returned. In addition, the visualisation can be parametrized to specific measurements by using the measurement_ids argument to only visualize a subset of the given data.

The following example will demonstrate the usage of the visualize-method as well as how to display only a single measurement and a subset. It should be noted, that the method returns an object to further optimize the plot to your needs.

import pyenzyme as pe

# Load the EnzymeML document at first
enzmldoc = pe.EnzymeMLDocument.fromFile("Model_4.omex")

Visualising all measurements#

Static#

By default the visualize-method returns a static scatterplot and by utilizing the use_names argument the species IDs will be converted to their actual names for an improved readability. Furthermore, trendlines can be added by using the trendline argument.

fig = enzmldoc.visualize(use_names=True, trendline=True)
../_images/output_4_0.png

Interactive#

Interactive visualisations behaves the same way and are returned when the interactive argument is set to True. These plots are based on Plotly and offer controls such as a Zoom, an Export as well as a selection of which species should be displayed.

enzmldoc.visualize(interactive=True, trendline=True, use_names=True)
../_images/output_6_1.png

It is not always desired to visualize all data but a single or subset of the given data. This can be done by using the measurement_idsargument, where measurement IDs are given as a list of strings. Since these apply to both interactive and static visualisations, the following will only display the interactive case for a single measurement.

# FYI: Measurement IDs always start with an "m"
enzmldoc.visualize(interactive=True, use_names=True, trendline=True, measurement_ids=["m1"])
../_images/output_8_0.png

One last thing#

If you are not sure about the ID of the measurements you’d like to visualize, use the printMeasurements-method in the EnzymeMLDocument object. It will not only display the IDs and names of your measurements, but also the initial concentrations assigned to each species.

enzmldoc.printMeasurements()

>>> Measurement m0: Cephalexin synthesis 1
    s0 | initial conc: 20.0 mmole / l       | #replicates: 1
    s1 | initial conc: 10.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 2.0 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m1: Cephalexin synthesis 2
    s0 | initial conc: 20.0 mmole / l       | #replicates: 1
    s1 | initial conc: 20.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 1.3 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m2: Cephalexin synthesis 3
    s0 | initial conc: 20.0 mmole / l       | #replicates: 1
    s1 | initial conc: 40.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 5.1 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m3: Cephalexin synthesis 4
    s0 | initial conc: 20.0 mmole / l       | #replicates: 1
    s1 | initial conc: 60.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 1.9 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m4: Cephalexin synthesis 5
    s0 | initial conc: 20.0 mmole / l       | #replicates: 1
    s1 | initial conc: 42.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 1.5 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m5: Cephalexin synthesis 6
    s0 | initial conc: 40.0 mmole / l       | #replicates: 1
    s1 | initial conc: 42.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 3.3 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m6: Cephalexin synthesis 7
    s0 | initial conc: 76.0 mmole / l       | #replicates: 1
    s1 | initial conc: 40.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 5.7 mmole / l        | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0
>>> Measurement m7: Cephalexin synthesis 8
    s0 | initial conc: 140.0 mmole / l      | #replicates: 1
    s1 | initial conc: 40.0 mmole / l       | #replicates: 1
    s2 | initial conc: 0.0 mmole / l        | #replicates: 1
    s3 | initial conc: 14.0 mmole / l       | #replicates: 1
    p0 | initial conc: 0.0002 mmole / l     | #replicates: 0