Characterization of Unique Components

This notebook demonstrates the tutorial workflow for MultiModulon analysis.

[1]:

# Import required libraries
from multimodulon import MultiModulon
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt

# Set display options
pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', 50)

Step 1: Load MultiModulon object

Load the saved MultiModulon object from Tutorial_1_Create_multiModulon_object.ipynb

[2]:

multiModulon = MultiModulon.load_json_multimodulon("./multiModulon_E_coli_comparison_demo.json.gz")

[3]:

multiModulon.species_palette

[3]:

{'BL21': '#B24C4C', 'MG1655': '#4C6AB2', 'W3110': '#88B24C'}

Step 2: Characterize Unique Components

Characterize Unique Components

MG1655

[4]:

multiModulon.view_iModulon_weights(
    species="MG1655",
    component="Unique_1",
    fig_size=(6, 4),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    show_COG=True
)

../_images/examples_characterization_unique_components_7_0.png

[5]:

multiModulon.view_iModulon_activities(
    species="MG1655",
    component="Unique_1",
    fig_size=(8, 3),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
)

../_images/examples_characterization_unique_components_8_0.png

BL21

[6]:

multiModulon.view_iModulon_weights(
    species="BL21",
    component="Unique_1",
    fig_size=(6, 4),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    show_COG=True
)

../_images/examples_characterization_unique_components_10_0.png

[7]:

multiModulon.view_iModulon_activities(
    species="BL21",
    component="Unique_1",
    fig_size=(8, 3),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    highlight_project = ['in_house_1', 'multi_ALE','pan_fur']
)

../_images/examples_characterization_unique_components_11_0.png

[8]:

multiModulon.view_iModulon_weights(
    species="BL21",
    component="Unique_3",
    fig_size=(6, 4),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    show_COG=True
)

../_images/examples_characterization_unique_components_12_0.png

[9]:

multiModulon.view_iModulon_activities(
    species="BL21",
    component="Unique_3",
    fig_size=(8, 3),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    highlight_project = ['in_house_2']
)

../_images/examples_characterization_unique_components_13_0.png

W3110

[10]:

multiModulon.view_iModulon_weights(
    species="W3110",
    component="Unique_2",
    fig_size=(6, 4),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf",
    show_COG=True
)

../_images/examples_characterization_unique_components_15_0.png

[11]:

multiModulon.view_iModulon_activities(
    species="W3110",
    component="Unique_2",
    fig_size=(8, 3),
    font_path = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
)

../_images/examples_characterization_unique_components_16_0.png