Viewing Atlas, CO, and Genotype cohorts in TVT
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The Trajectory Visualization tool (TVT) can be used to view all the patients within cohorts prepared with , , and .
In fact, TVT can be used to read in any cohort prepared with any tool (including R and Python) as long as the input file is correctly formed (as a tab-separated text file with a FINNGENID column, see ).
Output files from CO can be uploaded directly to TVT.
To visualize a CO cohort with TVT, first . Then open TVT and read the CO output file into TVT by clicking Browse... and selecting your CO output file from the folders.
Atlas cohorts can be exported to TVT from the Cohort drop-down menu in Data source. TVT reads the cohort directly from Atlas.
Output files from Genotype Browser can also be uploaded directly to TVT.
You also have the option to pre-process Genotype cohorts with the Cohort Operations tool before loading them into TVT. CO can be used to combine Atlas and Genotype Browser cohorts, and cohorts from a text file, in flexible ways.
Follow the instructions to view the data with TVT.
Another way to view Atlas cohorts in TVT is to first . Then open TVT and read the CO output file into TVT by clicking Browse... as above.
Follow the instructions to view the data with TVT.
To visualize a Genotype cohort with TVT, first . TVT can then read the raw Genotype Browser output files - click Browse... as above.
As an often-useful example, with the to form one file of unphased heterozygotes.
Further, a phenotype cohort (e.g. patients with a given disease, defined in Atlas) can then be divided into groups of homozygotes and heterozygotes for a given variant . With TVT pre-processed genotype cohorts .
Follow the instructions to view the data with TVT.
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