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Working with selections

jfnavarro edited this page Jun 15, 2020 · 5 revisions

Selections can be made in any dataset and they can be stored, exported and imported. The ST Viewer allows to work with selections and perform several analysis on them trough the "Selections" window that can be accessed trough "Views".

Typically, the selections window should look like this:

In this case there are 2 selections, one was exported from a file and the other one was created with the lasso selection.

There are multiple features in the Selections view, some are only available for 1 selection, some for 2 and some for more than 2.

  1. Shows a table with the spots and their total count of one selection
  2. Shows a table with the genes and their total count of one selection
  3. Shows the QC stats window of one selection
  4. Shows a correlation plot of two selections. The correlation will be computed for the accumulated gene counts (for all spots) and you may chose whether to use log scale or not. If you click on one dot in the correlation plot the gene corresponding to it will be shown in a box.
  5. Performs a differential expression analysis (DEA) between two selections
    • Select two selections and click on the DEA button
    • Chose what normalization method to use
    • Chose the settings for the thresholds
    • Chose a FDR and log2 fold-change values to define a high confidence threshold
    • Click on run (it may take some minutes...) Once the DEA has completed the differently expressed genes will be shown in the table which you can sort and query. High confident genes will be labeled in red, if you click on one gene in the table it will be marked in the volcano plot. The volcano plot shows all the differently expressed genes where the high confident ones are colored red. The list of high confident genes and the volcano plot can be exported to files.
  6. Merge multiple selections into one (useful for DEA for example)
  7. Import selections from files
  8. Export a selection to a file
  9. Edit a selection fields (name, comments, etc..)
  10. Remove a selection from the list