list_datasets.RdAll available datasets for the specified experiment(s), sample(s) or
dataset code(s) are retrieved as DataSet objects by
list_datasets(). Each dataset has a type and all realized type
identifiers can be listed using list_dataset_types(). A more compact
object type, uniquely identifying a DataSet, is that of a
DatasetIdentifier. Given either a set of DataSet objects or a character
vector holding (a) dataset code(s), list_dataset_id() fetches the
corresponding DatasetIdentifier objects. Behavior of the function
list_references(), in particular the returned object type, depends on
input types. For more information, please refer to the details section.
list_datasets(token, x, ...) # S3 method for Sample list_datasets(token, x, include = c(NA, "children", "parents", "all"), ...) # S3 method for Experiment list_datasets(token, x, include = c(NA, "children", "parents", "all"), ...) # S3 method for character list_datasets(token, x, include = c(NA, "children", "parents", "all"), ...) list_dataset_ids(token, x, ...) # S3 method for character list_dataset_ids(token, x, ...) # S3 method for DataSet list_dataset_ids(token, x, ...) list_references(token, x, ...) # S3 method for PlateIdentifier list_references(token, x, type = c("raw", "segmentation", "feature"), ...) # S3 method for Plate list_references(token, x, type = c("raw", "segmentation", "feature"), ...) # S3 method for PlateMetadata list_references(token, x, type = c("raw", "segmentation", "feature"), ...) # S3 method for Sample list_references(token, x, type = c("raw", "segmentation", "feature"), ...) # S3 method for MaterialGeneric list_references(token, x, experiment = NULL, ...) # S3 method for MaterialScreening list_references(token, x, experiment = NULL, ...) # S3 method for MaterialIdentifierGeneric list_references(token, x, experiment = NULL, ...) # S3 method for MaterialIdentifierScreening list_references(token, x, experiment = NULL, ...) # S3 method for DatasetIdentifier list_references(token, x, wells = NULL, channels, ...) # S3 method for DataSet list_references(token, x, wells = NULL, channels, ...) # S3 method for DatasetReference list_references(token, x, wells = NULL, channels, ...) # S3 method for FeatureVectorDatasetReference list_references(token, x, wells = NULL, channels, ...) # S3 method for FeatureVectorDatasetWellReference list_references(token, x, wells = NULL, channels, ...) # S3 method for ImageDatasetReference list_references(token, x, wells = NULL, channels, ...) # S3 method for MicroscopyImageReference list_references(token, x, wells = NULL, channels, ...) # S3 method for PlateImageReference list_references(token, x, wells = NULL, channels, ...) list_dataset_types(token, ...)
| token | Login token as created by |
|---|---|
| x | Object to limit search for datasets/files with. |
| ... | Generic compatibility. Extra arguments will be passed to
|
| include | String indicating whether to include parent/child datasets as well. |
| type | For listing image datasets, it can be specified, whether only raw image datasets, only segmentation image datasets or any kind of image datasets (default) are to be listed. |
| experiment | When searching for datasets associated with materials, the search can be limited to a single experiment. |
| wells | A (set of) |
| channels | A character vector with imaging channel names to limit the dataset listing to. |
Depending on the number of resulting objects, either a
json_class (single object) or a json_vec (multiple objects), is
returned. For the specific sub-class, refer to the Details section.
list_datasets() is an s3 generic function that can be dispatched on
Sample and Experiment objects, as well as character vectors containing
dataset codes and it returns sets of DataSet objects. Additionally it
can be requested that parent or child datasets are to be included as well.
Several classes in addition to DatasetIdentifier implement the
IDatasetIdentifier interface, including
DatasetReference
FeatureVectorDatasetReference
FeatureVectorDatasetWellReference
ImageDatasetReference
MicroscopyImageReference
PlateImageReference
The return type of list_references() depends on dispatch object type and
in some cases on additional arguments. If the s3 generic function
list_references() is dispatched on plate objects (Plate,
PlateIdentifier or PlateMetadata or Sample objects, representing
plates), ImageDatasetReference objects are returned (except if the type
argument is set to feature, in which case, if
MaterialIdentifierScreening objects are used as input,
PlateWellReferenceWithDatasets objects are returned, which each contain
ImageDatasetReference and FeatureVectorDatasetReference objects.
Whenever list_references() is dispatched on dataset ids or dataset
reference objects, the resulting object type depends on whether a (set of)
WellPosition object(s) were specified as wells argument. For its
default value (NULL), a set of MicroscopyImageReference objects is
returned, while PlateImageReference objects are returned otherwise.
The API function listDataSetsForSample()
has a parameter areOnlyDirectlyConnectedIncluded, which is currently
fixed to TRUE. The documentation contains the following explanation:
If true, only datasets that are directly connected to the sample are included, otherwise datasets of child samples are included as well.
This does however not seem to correspond to including child datasets in the
API call to listDataSets() via its connectionsToGet argument. As long
as it is not entirely clear how the inclusion of child/parent datasets
differs from setting areOnlyDirectlyConnectedIncluded to FALSE, this
option is not exposed to the user.
Other object listing functions: list_experiments,
list_material, list_plates,
list_projects, list_samples
# \donttest{ tok <- login_openbis() # search for a sample object corresponding to plate KB2-03-1I samp <- search_openbis(tok, search_criteria( attribute_clause("code", "/INFECTX_PUBLISHED/KB2-03-1I") ), target_object = "sample") # list all datasets associated with this plate ds <- list_datasets(tok, samp) # select a feature dataset, note how the fields "parentCodes" and # "childrenCodes" both are not set feat_ds <- ds[[grep("FEATURES_CC_MAT", get_field(ds, "dataSetTypeCode"))]] # fetch parent and child datasets and now both the "parentCodes" and # "childrenCodes" fields are populated with the corresponding codes feat_ds <- list_datasets(tok, get_field(feat_ds, "code"), include = "all") # re-using the plate sample from above, an ImageDatasetReference object # corresponding to the associated raw imaging dataset is listed raw_ref <- list_references(tok, samp) # available imaging channels are get_field(raw_ref, "properties")[["IMAGE.CHANNEL.LIST"]]#> [1] "Cy5,DAPI,GFP"# a more specific image reference object can be retrieved by passing a # well specification to list_references() well_ref <- list_references(tok, raw_ref, wells = well_pos(name = "A2"), channel = "DAPI") # a reference to 9 images is returned, as there are 3 x 3 imaging tiles # per well length(well_ref)#> [1] 9