Introduction

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After successfully uploading single-cell dataset, users are allowed to manipulate the cell and feature level annotations in the UI. The operation for the two types of annotation is distributed to two separated tabs, which work in the same way. This documentation will only describe the usage for the cell annotation tab.

Users can enter the interface as instructed by the screenshot above. With this interface, users can either upload extra annotations or edit existing annotations.

Here we will take the example PBMC3K dataset as an example. We imported this dataset through the “Data” -> “Import Single Cell Data” tab, by selecting “Import example datasets” first and using the default “PBMC 3K (10X)” option then.

Basic Operation

The whole tab consists of three parts: the editing area within “Options for editing and importing Cell Annotation data” panel, save/reset button, and the demonstration area within “Table of Cell Annotations” panel.

Users can start with making any type of operation at within “Options for editing and importing Cell Annotation data” panel. The detail of each type of operation will be described later. After clicking on “Confirm XX” button that follows the specific inputs, the effect will be immediately shown in the “Table of Cell Annotations”. It is important to know that this table is just for demonstration of the result. Simply clicking on a “Confirm” button does not take any direct effect to the background data object.

After any changes are confirmed, users must click on “Save” button to take them into effect. A “Reset” button is also provided in case any unwanted operation happens. When users click on the “Reset” button, the annotation table will be reset to the status after the last time users “save” any change. Or if no change is “saved”, it will be reset to the original status.

Import New Annotation from File

TODO

Edit Existing Annotation

Bins

TODO

Merge columns

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Users can merge any two columns that exist in the cell annotation table. SCTK merges them in a direct concatenate manner, with allowing setting a customized separator. As shown in the screenshot above, user should enter the “Merge Columns” tab to access this functionality. Different values should be selected for the “Select first column” and Select second column" input. The order of these selections matters as it will determine how the values are ordered in the merged field. It is recommended that users set an _ (underscore) or a - (dash) as the input for “add separator between merged values”. Setting a (space) here will not trigger any direct error but is not a best practice. After determining all the three inputs, users should click on “Confirm Merge” button to make the change. The effect can be immediately observed in the “Table of Cell Annotations” at the bottom, as shown in the lower part of the screenshot above.

Magic Fill

TODO

Clean

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Users can clean up a selected column by removing any “alphabets”, “digits”, “spaces”, or “symbols” from all the values in this column. First users will need to specify the column at “Select attribute column”, and choose what type of clean-up should be performed at “select removal criteria”. Then users must click on “Confirm Clean” to enable the change. The effect can be immediately observed in the “Table of Cell Annotations” at the bottom, as shown in the lower part of the screenshot above.

Add column

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Users can add a new column where all values are the same. Users will need to define the name of the new column at “enter new empty column name”, and the value of this column at “default value to fill”. Then users need to click on “Create Column” make the change. The effect can be immediately observed in the “Table of Cell Annotations” at the bottom, as shown in the screenshot above.

Delete column

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User can remove an entire column. The unwanted column can be deleted by simply selecting the name of the column at “select attribute to delete” and click on the “Delete” button. The effect can be immediately observed in the “Table of Cell Annotations” at the bottom, as shown in the screenshot above.