Viewing Atlas, CO, and Genotype cohorts in TVT
Last updated
Last updated
The Trajectory Visualization tool (TVT) can be used to view all the patients within cohorts prepared with Atlas, Cohort Operations (CO), and Genotype browser.
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 Running TVT).
Output files from CO can be uploaded directly to TVT.
To visualize a CO cohort with TVT, first export the cohort from CO. Then open TVT and read the CO output file into TVT by clicking Browse... and selecting your CO output file from the folders.
Follow the instructions here to view the data with TVT.
Atlas cohorts can be exported to TVT from the Cohort drop-down menu in Data source. TVT reads the cohort directly from Atlas.
Another way to view Atlas cohorts in TVT is to first extract the cohort from Atlas using CO. Then open TVT and read the CO output file into TVT by clicking Browse... as above.
Follow the instructions here to view the data with TVT.
Output files from Genotype Browser can also be uploaded directly to TVT.
To visualize a Genotype cohort with TVT, first output the genotype files using Genotype Browser. TVT can then read the raw Genotype Browser output files - click Browse... as above.
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.
As an often-useful example, with the Cohort Operations tool heterozygotes (0|1 and 1|0) can be combined 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 using CO. With TVT pre-processed genotype cohorts can then be visualized in a similar way as any CO cohort.
Follow the instructions here to view the data with TVT.
You may also find Example: Visualizing Genotype Browser output data with TVT useful.
