How to find samples that you want to remove or keep in the view. How to make subgroups.
Use the search box at the top of the screen to first pick/find your samples of interest. Then filter to keep or removes these samples, create a new subgroup column, or zoom.
The bar highlighted above allows you to search all data on the screen for your search term. Note that it will not search data that is not on the screen. Samples that match your criteria are marked with a black bar in the Visual Spreadsheet.
Searching for samples
You can search for samples by either typing in the search bar or by clicking on the dropper icon to enter the pick samples mode. The pick samples mode will allow you to click on a column to select samples. The search term for your picked samples will appear in the search bar. To exit the pick samples mode, click on the dropper icon again.
Once you have your sample(s) of interest, click on the filter + subgroup menu and choose to:
Keep samples: Keep only the samples which match your criteria.
Remove samples: Remove the samples which match your criteria.
Clear sample filter: Remove ALL filters currently applied.
Remove Samples with nulls: Removes samples that have no data for one or more columns. Equivalent to typing 'null' in the search bar and choosing 'Remove samples'.
Zoom: Zoom to the samples that meet your criteria. Shift-click to zoom out.
New subgroup column: Create a new column where samples that meet your criteria are annotated as 'true' and samples that don't meet your criteria are annotated as 'false'. This new columns can then be used for Kaplan Meier Analysis or in the Chart View.
Once you have either filtered, created a subgroup column, or zoomed to samples, your search term will be added to the search history. Access the search history by clicking the downward facing arrow at the upper right of the search bar.
Note this search history will be preserved in bookmarks.
Changing subgroup labels
Once the subgroup column is created, users can change the labels from "true" or "false" to, for example, "wild type" or "EGFR mutant" by adjusting the column display settings. To access these select the three dot menu at the top of the column and choose 'Display'