Awesome Kreport Charts

Create awesome charts for kreports (kraken-style reports). The following charts are available:

• sankey
• sunburst_no_values
• sunburst_values
• treemap

There are some chart examples at samples_files folder.

It is possible to show all domains, or select some domain to show (Viruses, Bacteria, Archaea or Eukarya). You can also apply filters such as minimum reads/contigs and exclude taxons.

To know more about kreports: https://ccb.jhu.edu/software/kraken/MANUAL.html#output-format

Multi Kreport File

It is possible to generate a consolidate kreport file from multiple samples using the following script:

https://github.com/jenniferlu717/KrakenTools/blob/master/combine_kreports.py

Example of usage:

Download the merging script at https://raw.githubusercontent.com/jenniferlu717/KrakenTools/master/combine_kreports.py and run the following command (adapt the command to your sample files):

python combine_kreports.py --only-combined --no-headers --report-files sample1.kreport sample_2.kreport sample_3.kreport -o merged.kreport

The consolidated kreport can be used as input for awesome_kreports_charts tool.

Instalation

Install with pip:

pip install awesome-kreport-charts

More info: https://pypi.org/project/awesome-kreport-charts/1.2.0/

Install from source:

git clone https://github.com/taniagmangolini/awesome-kreport-charts.git

cd awesome_kreport_charts

python3 setup.py install

Help

Use the following command to see all the options:

python main.py --helṕ

History

• 0.0.1: first release
• 0.0.2: add project info
• 1.0.0: add sunburst chart
• 1.1.0: add sunburst_values and sunburst_no_values charts, fix sunburst values to child values and all domains.
• 1.1.1: style fixes
• 1.1.2: add chart abstract class and merging kreports option.
• 1.2.0: add chart treemap chart.

Usage as a command line tool

python3 awesome_kreport_charts -mb 1000 -mv 5 --exclude 9606 8959 -o sample_files/sankey-all.html -- sample_files/sample.kreport

python3 awesome_kreport_charts --min_bacteria 10 --c sunburst_no_values -o sample_files/sunburst__no_values_all.html -- sample_files/sample.kreport

python3 awesome_kreport_charts --min_bacteria 10 --c sunburst_values -o sample_files/sunburst__values_all.html -- sample_files/sample.kreport

python3 awesome_kreport_charts --min_bacteria 10 --c treemap -o sample_files/treemap__all.html -- sample_files/sample.kreport

Import as a package

You can import it to your own project and generate the charts as the example below:

from awesome_kreport_charts.models.command import CommandSet
from awesome_kreport_charts.utils.file_processor import KreportProcessor
from awesome_kreport_charts.charts.sankey_chart import SankeyChart
from awesome_kreport_charts.charts.sunburst_chart import SunBurstChart


commands = CommandSet(kreport_file='sample_files/sample.kreport',
                      domain=None,
                      excluded_nodes=[],
                      min_viruses=1,
                      min_bacteria=100,
                      min_archaea=1,
                      min_eukarya=1,
                      min_level='S',
                      chart_type='sankey',
                      output_path='sample_files/sample.html')

kreport_processor = KreportProcessor(commands)
kreport_processor.process_kreport()

if commands.chart_type == 'sankey':
    chart = SankeyChart(kreport_processor.kreport, commands)
if commands.chart_type == 'sunburst':
    chart = SunBurstChart(kreport_processor.kreport, commands)
chart.plot()