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KEGGaNOG Usage Guide

INSTALLATION

conda create -n kegganog pip -y
conda activate kegganog
pip install kegganog

HELP

! KEGGaNOG -h

Usage: KEGGaNOG [OPTIONS]                                                      
                                                                                
 KEGGaNOG: Link eggNOG-mapper and KEGG-Decoder for pathway visualization.       
                                                                                
╭─ Options ──────────────────────────────────────────────────────────────────────────────╮
│ --input      -i         TEXT                    Path to eggNOG-mapper annotation file. │
│ --output     -o         TEXT                    Output folder to saveresults.          │
│ --multi      -M                                 Run KEGGaNOG in multi-sample cohort    │
│                                                 profile mode.                          │
│ --overwrite  -overwrite                         Overwrite the output directory if it   │
│                                                 already exists.                        │
│ --dpi        -dpi       INTEGER                 DPI resolution mapping index for the   │
│                                                 output image visualization.            │
│                                                 [default: 300]                         │
│ --color      -c         [Blues|Greens|Reds|     Target seaborn color map palette       │
│                         Purples|Greys|Oranges]  matrix rule.                           │
│                                                 [default: Blues]                       │
│ --name       -n         TEXT                    Sample identity text string for        │
│                                                 axis labeling.                         │
│                                                 [default: SAMPLE]                      │
│ --group      -g                                 Group the pathway matrix heatmap rows  │
│                                                 based on predefined functional         │
│                                                 categories.                            │
│ --web                                           Launch the interactive local web UI    │
│                                                 dashboard at http://localhost:8000.    │
│ --version    -V                                 Show version and exit.                 │
│ --help       -h                                 Show this message and exit.            │
╰────────────────────────────────────────────────────────────────────────────────────────╯

USAGE EXAMPLE

Single MODE

As the demo data for this usage guide eggNOG-mapper output of Lpb. plantarum IS-10506 is used
It is a probiotic from I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506 study

First, download the demo data

Input

! wget https://github.com/iliapopov17/KEGGaNOG/raw/refs/heads/dev/demo_data.zip && \
    unzip demo_data.zip && rm -rf demo_data.zip

Then run KEGGaNOG

Input

! KEGGaNOG -i demo_data/LaPla/LaPla.emapper.annotations -o LaPla

By the key -i the input (eggNOG-mapper output file) must be provided By the key -o the path to output directory (it will be created if it does not exist) must be provided

The resulted figure:

The dpi of the resulted heatmap can be adjusted by using -dpi key
300 dpi is used by default

The color of the heatmap can be adjusted by using -c key
'Blues' are used by default

The sample name can be adjusted by using -n key
'SAMPLE' is the default sample name
It supports regular expressions, so to make some words in italics (e.g.: Lpb. plantarum IS-10506) please use $\it{Lpb. plantarum}$ IS-10506

This is not recommended while using CLI functionality of KEGGaNOG — using regular expressions for sample naming can be more helpful in Heatmap API

Grouping

Alternatively, all the pathways can be grouped by their functions using -g key — gaps between groups will be added on the heatmap

Input

! KEGGaNOG -i demo_data/LaPla/LaPla.emapper.annotations -o LaPla_grouped -c Greens -g -n 'Lpb. plantarum IS-10506'

The resulted figure:

Multi MODE

As the demo data for this usage guide eggNOG-mapper output of:

• Acidilobus saccharovorans 345-15 — AciSa
• Bacillus subtilis subsp. subtilis str. 168 — BaSu
• Bacteroides thetaiotaomicron VPI-5482 — BaThe
• Clostridium acetobutylicum ATCC 824 — CloAce
• Lactiplantibacillus plantarum strain IS-10506 — LaPla
• Meiothermus ruber DSM 1279 — MeRu
• Pseudomonas putida KT2440 — PsePu
• Sorangium cellulosum So0157-2 — SoCe
• Staphylococcus carnosus subsp. carnosus TM300 — StaCa
• Thermotoga maritima MSB8 — TheMa
  

are used

The demo has been already downloaded (if not — run the code below)

Input

! wget https://github.com/iliapopov17/KEGGaNOG/raw/refs/heads/dev/demo_data.zip && \
    unzip demo_data.zip && rm -rf demo_data.zip

Create a list file for KEGGaNOG -M input

Input

! ls demo_data/*/*.emapper.annotations > demo_data/listFile.txt

Then run KEGGaNOG

Input

! KEGGaNOG -M -i demo_data/listFile.txt -o multi

By the key -i the input (eggNOG-mapper output file) must be provided
By the key -o the path to output directory (it will be created if it does not exist) must be provided

The resulted figure:

The dpi of the resulted heatmap can be adjusted by using --dpi key
300 dpi is used by default

The color of the heatmap can be adjusted by using -c key
'Blues' are used by default

The order of samples in multi-sample heatmap can be adjusted by using Heatmap API

Grouping

Alternatively, all the pathways can be grouped by their functions using -g key — gaps between groups will be added on the heatmap

Input

! KEGGaNOG -M -i demo_data/listFile.txt -o multi_grouped_color -c Greens -g

The resulted figure: