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Hi Mark,
Ok, thank you.
Divya
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Subject: [EXT] Re: [milaboratory/mixcr] lineage tree plot from a samples collected at a single datapoint (error Timepoint) (Discussion #1917)
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Hi,
Unfortunately, the visualization capabilities of SHM trees are quite limited. For your tasks, I recommend using our latest software, Platforma<https://platforma.bio/>. If you have any questions about how to use it, please post them in our community discourse<https://community.platforma.bio/>.
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Hi, I am plotting the lineage tree via following script in MIXCR/4.7.0:
metadata:
sample Timepoint Subset
E2-SUBJ059-IgM_S13_L001 d21 IgM
script:
mixcr exportPlots shmTrees
-m "/mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS/lineage_tree/metadata.tsv"
--node-color Timepoint
--line-color Subset
--ids 5019
"/mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS/lineage_tree/E2-SUBJ059-IgM_S13_L001.shmt"
"/mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS/lineage_tree/figs1/E2_SUBJ059_IgM_S13_Clone_id5019.pdf"
plot i generated is:
E2_SUBJ059_IgM_S13_Clone_id5019.pdf
Concerns:
- When i read the mixcr documentation about creating the metadata on https://mixcr.com/mixcr/guides/ig-trees-reconstruction/?h=mixcr+lineage+tree#export-lineage-trees-in-a-tabular-format the metadata contains multiple samples and when i ran the script with metadata with multiple samples i did not get results. The figure I generated right now has node points but there is no log of distance from germline, or distinguished colours of node point. I want to know the under the hood mechanism. Ideally my nodes should be connected either via isotypes or via time points, since i do not have timepoints then the nodes should be connected via isotypes, however providing the isotypes in the code does not generate the appropriate results.
<style> </style>The structure of my SHMT table is:
Divya
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