Coerce an object into a SingleCellExperiment
Coerce a tof_tbl into a SingleCellExperiment
Usage
as_SingleCellExperiment(x, ...)
# S3 method for class 'tof_tbl'
as_SingleCellExperiment(
x,
channel_cols = where(tof_is_numeric),
reduced_dimensions_cols,
metadata_cols = where(function(.x) !tof_is_numeric(.x)),
split_reduced_dimensions = FALSE,
...
)Arguments
- x
A tof_tbl
- ...
Unused.
- channel_cols
Unquoted column names representing columns that contain single-cell protein measurements. Supports tidyselect helpers. If nothing is specified, the default is all numeric columns.
- reduced_dimensions_cols
Unquoted column names representing columns that contain dimensionality reduction embeddings, such as tSNE or UMAP embeddings. Supports tidyselect helpers.
- metadata_cols
Unquoted column names representing columns that contain metadata about the samples from which each cell was collected. If nothing is specified, the default is all non-numeric columns.
- split_reduced_dimensions
A boolean value indicating whether the dimensionality results in x should be split into separate slots in the resulting
SingleCellExperiment. If FALSE (the default), the split will not be performed and thereducedDimsslot in the result will have a single entry ("tidytof_reduced_dimensions"). If TRUE, the split will be performed and thereducedDimsslot in the result will have 1-4 entries depending on which dimensionality reduction results are present in x ("tidytof_pca", "tidytof_tsne", "tidytof_umap", and "tidytof_reduced_dimensions"). Note that "tidytof_reduced_dimensions" will include all dimensionality reduction results that are not named according to tidytof's pca, umap, and tsne conventions.