Merge pull request #258 from AlexsLemonade/sjspielman/254-adt-rowdata…

…-docs

Update adt altExp rowData docs

docs/merged_objects.md

@@ -77,7 +77,7 @@ The following per-cell data columns are included for each cell, calculated using
 | `submitter_celltype_annotation`  | If available, cell type annotations obtained from the group that submitted the original data. Cells that the submitter did not annotate are labeled as `"Submitter-excluded"`                                                                                                                                                                                   |
 | `singler_celltype_annotation`    | If cell typing with `SingleR` was performed, the annotated cell type. Cells labeled as `NA` are those which `SingleR` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"`                                    |
 | `singler_celltype_ontology`      | If cell typing with `SingleR` was performed with ontology labels, the annotated cell type's ontology ID. Cells labeled as `NA` are those which `SingleR` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"` |
-| `cellassign_celltype_annotation` | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"`. If `CellAssign` was unable to complete successfully for a given library, cells will be labeled as `Not run`                        |
+| `cellassign_celltype_annotation` | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"`. If `CellAssign` was unable to complete successfully for a given library, cells will be labeled as `"Not run"`                        |
 | `cellassign_max_prediction`      | If cell typing with `CellAssign` was performed and completed successfully, the annotation's prediction score (probability)                                                                                                                                                                                                                                                                 |
 
 
@@ -295,6 +295,7 @@ The columns `mean-SCPCL000000` and `detected-SCPCL000000` are present for each l
 
 | Column name | Contents                                                       |
 | ----------- | -------------------------------------------------------------- |
+| `adt_id`  | Name or ID of the ADT                                              |
 | `mean-SCPCL000000`      | Mean ADT count across all cells/droplets. Only present for libraries with CITE-seq data                       |
 | `detected-SCPCL000000`  | Percent of cells in which the ADT was detected (ADT count > 0 ). Only present for libraries with CITE-seq data |
 | `target_type` | Whether each ADT is a target (`target`), negative/isotype control (`neg_control`), or positive control (`pos_control`). If this information was not provided, all ADTs will have been considered targets and will be labeled as `target` |

docs/sce_file_contents.md

@@ -89,7 +89,7 @@ Further, if cell type annotation was performed, there will be additional columns
 | `cluster`  | Cell cluster identity identified by graph-based clustering |
 | `singler_celltype_annotation`  | If cell typing with `SingleR` was performed, the annotated cell type. Cells labeled as `NA` are those which `SingleR` could not confidently annotate |
 | `singler_celltype_ontology`  | If cell typing with `SingleR` was performed with ontology labels, the annotated cell type's ontology ID. Cells labeled as `NA` are those which `SingleR` could not confidently annotate |
-| `cellassign_celltype_annotation`  | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If `CellAssign` was unable to complete successfully, cells will be labeled as `Not run`  |
+| `cellassign_celltype_annotation`  | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If `CellAssign` was unable to complete successfully, cells will be labeled as `"Not run"`  |
 | `cellassign_max_prediction`  | If cell typing with `CellAssign` was performed and completed successfully, the annotation's prediction score (probability)  |
 
 ### SingleCellExperiment gene information and metrics
@@ -260,6 +260,7 @@ This data frame contains the following columns with statistics for each ADT:
 
 | Column name | Contents                                                       |
 | ----------- | -------------------------------------------------------------- |
+| `adt_name`  | Name or ID of the ADT                                          |
 | `mean`      | Mean ADT count across all cells/droplets                       |
 | `detected`  | Percent of cells in which the ADT was detected (ADT count > 0 ) |
 | `target_type` | Whether each ADT is a target (`target`), negative/isotype control (`neg_control`), or positive control (`pos_control`). If this information was not provided, all ADTs will have been considered targets and will be labeled as `target` |