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Annotations

jlchang edited this page Feb 25, 2020 · 1 revision

Creating and sharing Single Cell Portal annotations

You can annotate cell populations during or after the creation of a Single Cell Portal study. If a study already exists, anyone who can view the study can directly annotate cell groups using Single Cell Portal tools. Additionally, you can share these new annotations with other portal users. This document provides step-by-step instructions for annotating existing Single Cell Portal studies.

Creating annotations: Step-by-step instructions

1. Log into Single Cell Portal using your Google account.

2. Click on the study you would like to annotate.

This will direct you to the Study Summary Page.

3. Select the "Explore" tab at the top of the page.

4. Verify that the study's Explore page has a cell ordination/scatter plot visualization.

This plot will be necessary for making the annotations. If it exists, proceed by selecting the three, horizontal bar drop-down menu to the left of the page. This will open a list of advanced tools.

5. Select "Create Annotations".

6. Click on the "Select Cells" button.

7. Label the group of annotations with a unique name.

In this example, we write "demo-two-groups".

8. Use the lasso or box tools to select cells of interest.

9. Label the selected and unselected cells.

On the left of the page, you will be prompted to label the selected and unselected cells. In this example, we select an arbitrary cell population and label it "inner". If you would like to lasso more cell populations, continue selecting cells. Each time you lasso a cell population, a new label option will appear to the left. Repeat the process as needed. When done, name the unselected group of cells. Here, we label the unselected cells "peripheral".

10. Click "Create Annotations" to save the annotations.

11. Refresh the explore tab and select the "View Options" gear icon.

The easiest way to refresh is to click on the "Summary" tab, then the "Explore" tab again. Then, select the "View Options" icon to the right of the page.

12. Click on the "Select Annotation" drop-down menu.

Select your annotation group (i.e. "demo-two-groups").

13. View the annotations.

These visualizations are private to you, only you may see them after logging in.

Annotating cell populations by gene expression

You can identify cell populations using gene expression patterns. In this case, you would first query a gene to view expression and then use the lasso tool on the resulting scatter plot of expression.

1. From the explore tab, go to the search bar and type in a gene of interest.

In the example below, we search for cells expressing the gene "Gad2".

2. Select the plot's scatter tab.

You can then use a lasso or box to annotate the cells of interest, using the same steps described above.

Managing, sharing, and publishing annotations

Annotations are private and can only be seen by study page owners. You do have the option of deleting and sharing those annotations.

Accessing and managing annotations from Single Cell Portal

1. Select the profile drop-down menu in the upper right-hand corner.

2. Select "My Annotations".

This will direct you to an annotations page with options to edit, download, and publish each set of annotations.

The delete button allows you to delete your annotation (but not the associated study), and the edit button allows you to change label names and share the annotation group. If you are the owner of both the annotation and the study form which it came, you will have an option to publish the annotations. This will add the annotations to the original study and make them public, private, or shared based on the permissions of the study.

Sharing annotated studies

You can share a study to which you've added annotations.

1. From the annotation list page, select the edit option for the annotations you want to share.

2. Select the Share Study button.

You will be prompted to add your collaborator's email and a permission type. Note that "View" allows a collaborator to view the annotations and "Edit" allows them to manage the annotation (eg. deleting, editing, sharing).

4. Select "Submit" to save the new permissions.

Questions and Feedback

For questions or to provide feedback, please email the Single Cell Portal team.

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