Highlight, Filter and Custom Groups of Samples
Want to only view only a subset of samples within a dataset?
Want to define your own groups for KM plots and other analyses?
Here are the steps taken in the walk-through:
- Select the TCGA BRCA cohort
- Select TP53 expression and mutation
- Find samples where column B (expression) is less than 10 (i.e. have relatively low expression)
- Find samples that have a nonsense or frame_shift mutation for TP53
- Filter down to just these samples
- Clear this filter
- Subgroup. Make a new column where the highlighted samples are marked as 'true' and those that are not are marked as 'false'.
- Examine new subgroups in Chart mode
Use the box below (in red) to first select/highlight your samples of interest and then either zoom, filter to just these samples, or create a new column.
This bar allows you to search all displayed columns for your search term of interest (ie. 'female' in a gender column). You can also enter your sample ID to see where your sample of interest falls in the plot. Samples that match your criteria are highlighted and then marked with a black bar.
Once you have your sample(s) of interest, click on the filter button (next to 'Matching samples: XXX') to remove samples that don't match your criteria. You can also choose from the options in the caret menu next to it to:
Filter: remove samples which do not match your criteria
Zoom: zoom to the samples that meet your criteria. Shift-click to zoom out.
New 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 is a great way to define your own criteria for a KM plot
Here are a few examples of how you might use this feature: