Running TVT

Timeline visualization example: Asthma

The data in this example is artificial mock data and does not show any real cases.

Tutorial video about TVT

FinnGen data users meeting 22nd Feb 2022 recording at 38min 09sec.

Tip: TVT works well together with the Cohort Operations tool. Cohort Operation tool can be used to build interesting cohorts then further explored with TVT. For example, CO can combine genotype data from Genotype Browser and phenotype data from Atlas. Data from TVT can also be exported for further modifications with CO. See also an Example workflow for survival time/endpoint analysis.

To run TVT efficiently, select at least an Advanced machine (16 CPUs, 128 GB memory) when starting Sandbox.

Step 1:

Then open TVT from the Sandbox Applications menu.

Step 2:

In TVT select the data freeze and cohorts you plan to use. Cohorts can be uploaded from Atlas or from a text file. Output files from the Genotype Browser can be read into TVT directly. Atlas cohorts are also available from the Cohort dropdown menu (see figure below). If loaded from a file (Browse...), the file must be tab-separated and contain one column of FinnGen IDs titled "FINNGENID".

The TVT works well together with the Cohort Operations tool. Cohorts exported as a text file from CO can be uploaded directly to the TVT.

Step 3:

Next select glyph segments for your data. In Atlas, glyph segments are introduced as Concept sets. In the Encoding menu, select glyph segment orientation (e.g. Top left), concept set, and the displayed color for glyph segments.

To restrict the search to certain registries select the registries you like from the visit type menu. If left black all registers in detailed longitudinal data are included. Check whether your concept set in Atlas is standard or non-standard. If the concept is non-standard tap the non-standard box under visit type(s).

Step 4:

After the glyph segment settings are done Extract the data from the Extract button. You can also make all glyph segment settings first and then extract all glyph segments at once by clicking the Extract all -button.

You can save your glyph segment settings for later use from the Save snapshot menu. Give a unique name for each snapshot. Snapshots with duplicated names are not saved.

Previously saved glyph segments (concept sets in Atlas) can be uploaded from the Read snapshot -> Select file -dropdown menu. Previously created glyphs can be reloaded from Read glyph from snapshot -> Select file menu.