TCRcloud is a TCR repertoire visualization and comparison tool
Project description
TCRcloud is a TCR repertoire visualization and comparison tool
Instalation
TCRcloud is written in python and can be installed from PyPI using pip:
pip3 install TCRcloud
Currently it is only compatible with linux-64 and osx-64 because one of the dependencies used is also only compatible with those operating systems. It does work on WSL if you want to use Windows.
TCRcloud uses the AIRR Data Commons API and needs AIRR compliant data as input
Usage
To create a word cloud
TCRcloud cloud AIRR_rearrangements_file.tsv
By default TCRcloud colours the CDR3 based on the Vgene but you can provide a json file that atributes colours in Hex format to specific sequences:
{
"#FF0000":["CAASITGNQFYF","CAVREDGTSGSARQLTF"],
"#0000FF":["CAVMDSNYQLIW"]
}
The sequences not in the file will be coloured grey.
To use your custom colours for the word cloud
TCRcloud cloud AIRR_rearrangements_file.tsv -c colours.json
To create a word cloud without a legend
TCRcloud cloud AIRR_rearrangements_file.tsv -l False
To create a radar plot comparing diversity metrics
TCRcloud radar AIRR_rearrangements_file.tsv
By default TCRcloud uses repertoire_id but you can create a legend with the text you want by providing a json file:
{
"2839362682105696746-242ac113-0001-012":"Twin 2A",
"2939134772391776746-242ac113-0001-012":"Twin 2B"
}
To create a radar plot with your desired legend
TCRcloud radar AIRR_rearrangements_file.tsv -c legend.json
To create a radar plot without a legend
TCRcloud radar AIRR_rearrangements_file.tsv -l False
Using TCRcloud you can download rearragements files from the AIRR compliant databases based on AIRR repertoire metadata files
To download AIRR rearrangements files
TCRcloud download AIRR_repertoire_file.json
TCRcloud provides some test data to experiment the tool. The data is one twin pair from the monozygotic twins study from the Mark Davis lab (DOI: 10.1038/ncomms11112)
To download the test data repertoire file
TCRcloud testdata
After having the testdata.airr.json file you can use the download function included in TCRcloud to get the matching rearragements file.
Examples:
TRA CDR3 word cloud
TRB CDR3 word cloud
TRG CDR3 word cloud
TRD CDR3 word cloud
Diversity comparison
Comparing here the αβ repertoire from one twin pair from the monozygotic twins study from the Mark Davis lab (DOI: 10.1038/ncomms11112)
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