Import Cell Annotations
The Import Cell Annotations tool can import annotations for each cell. The importer produces Cell Annotations (
) that can be used to define groups of cells for use in many tools such as Differential Expression for Single Cell. Cell Annotations can also be visualized in a Dimensionality Reduction Plot.
Often the same file can be imported as either Cell Clusters or Cell Annotations. The principal advantage of Cell Annotations is that they can represent numerical data. An example might be the probability of a cell being in a particular cell cycle phase.
The importer can be found here:
Import (
) | Single Cell Data (
) | Import Cell Annotations (
).
The following options are available:
- Data file. A single file in .csv, .tsv or .xlsx format. The first row in the file is a header. Each subsequent row describes a cell. Empty lines are ignored.
- First column defines sample. When this is enabled, the sample name and barcode are read from the first and second columns in the file, respectively. Otherwise, the first column is used to extract the barcode and optionally the sample, as defined in Cell format. Subsequent columns represent categories containing information about the cells.
- Cell format and Sample. How cells are identified, see Cell format in importers for more details.
- Matrix (Optional). When a matrix is supplied, the sample name is taken from the matrix. If the previous options also provide sample names:
- If different from the matrix, the importer fails with an error. This can be useful when checking that the file being imported matches the supplied matrix.
- Rows in the file describing cells that are not in the matrix are skipped.
Note that the sample name can only be set using only one of the First column defines sample, Cell format, or Sample options. The Matrix option is mandatory if none of the previous options is used for defining the sample and then the matrix must be for one sample only.