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Cluster_RGI_heatmap.eps
Cluster_RGI_heatmap.png
Cluster_Resistance_Mechanism_RGI_heatmap.eps
Cluster_Resistance_Mechanism_RGI_heatmap.png
Drug_Class_Frequency_RGI_heatmap.eps
Drug_Class_Frequency_RGI_heatmap.png
Gene_Family_RGI_heatmap.eps
Gene_Family_RGI_heatmap.png
PrintCSV.py
Profile_Frequency_RGI_heatmap-41.eps
Profile_Frequency_RGI_heatmap.png
README.md
STD.png
WriteCSV.py
WriteCSV_binary.py
Z.png
binaryOutput.csv
dendrogramHeatMap.py
generateDatasets.py
generateDatasetsParallelProcessing.py
heatMap.py
out.csv
output.csv

README.md

Resistance Gene Identifier (RGI) for E. coli (Bacteria)

Code Description

1. Generate Datasets (JSON)

Step 1.1: Basic Process [ Generate Datasets ]
Step 1.2: Parallel Processing [ Generate Datasets ]

Note: The programme will take FASTA sequences as inputs; it will produce JSON file for each sequence.

 

2. HeatMap:

Step 2.1 Heatmap [ HeatMap ]

Note: The programme will take previously generated JSON file as inputs; it will produce heatmap.

 

3. Generate Datasets (CSV)

Step 3.1 [ Generate Percentage CSV ]
Step 3.2 [ Generate Binary CSV ]

Note: The programme will take previously generated JSON file as inputs; it will produce the name of antibiotic resistance ontology (ARO) and the percentage of identity for each ARO.

Step 3.3 Visualize Datasets

Please click here to visualize the CSV file (percentage).

Please click here to visualize the CSV file (binary).

 

4. Dendrogram with HeatMap:

Step 4.1 [ Draw Dendrogram HeatMap ]

Note: The programme will take previously generated CSV file as input; it will produce dendrogram with heatmap.

 

HeatMap ( Command-line )

Step 1: Default

rafsanjani@mrz:~$ rgi heatmap --input PATH

Step 2: Gene Family

rafsanjani@mrz:~$ rgi heatmap --input PATH --category gene_family --display text

Step 3: Profile Frequency

rafsanjani@mrz:~$ rgi heatmap --input PATH --frequency

Step 3: Drug Class Frequency

rafsanjani@mrz:~$ rgi heatmap --input PATH --category drug_class --frequency --display text

Step 4: Cluster

Step 4.1: Default Cluster
rafsanjani@mrz:~$ rgi heatmap --input PATH --cluster both
Step 4.2: Cluster on Resistance Mechanism
rafsanjani@mrz:~$ rgi heatmap --input PATH --cluster samples --category resistance_mechanism --display text

 

Heatmap ( Image )

Gene Family RGI Heatap

Cluster RGI Heatmap

Profile Frequency RGI Heatmap

Cluster RGI Heatmap

Drug Class Frequency RGI Heatmap

Cluster RGI Heatmap

Cluster RGI Heatmap

Cluster RGI Heatmap

Cluster Resistance Mechanism RGI Heatmap

Cluster RGI Heatmap

 

Dendrogram with Heatmap ( Image )

Dendrogram with Heatmap

STD

 

Color Code

  • Yellow represents a perfect hit,
  • Teal represents a strict hit,
  • Purple represents no hit.
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