v0.4.0

SingleCellProjections v0.4.0

Diff since v0.3.9

Breaking

• DataMatrix will now always use the first column of var/obs annotations as ID. (Multiple ID columns are no longer supported.)
• load_counts - The default obs ID column name is now "cell_id" (was "id" before).
• load10x - default to using only first column (id) as unique identifier. Specify e.g. var_id="var_id"=>["id", "feature_type"] to merge multiple columns to create the ID.
• load10x - default to using first column (barcode) as unique identifier.
• load10x - no longer supports copy_obs_col kwarg.
• set_var_id_cols! is replaced with set_var_id_col! (since there is only one ID column).
• set_obs_id_cols! is replaced with set_obs_id_col! (since there is only one ID column).
• Update to SCTransform 0.2, which handles logcellcounts better when there are multiple modalities (e.g. RNA and antibody counts) present in the data.

Added

• var_counts_fraction - Just like var_counts_fraction!, but not modifying the object in place.
• var_counts_sum and var_counts_sum! - For summing over selected variables. Useful for counting e.g. total RNA expression and finding number of expressed features.
• Added support for using external annotations where applicable (filter, transforms, normalization, statistical tests, var_counts_fraction!, var_counts_sum!)
• Added experimental (thus yet unexported) Annotations struct, that wraps a DataFrame with IDs in the first column, and ensures that ID remain when accessing columns. (So that the resulting object can be leftjoined to data.obs/data.var.)

Fixed

• Add compat for weakdeps (UMAP, TSne, PrincipalMomentAnalysis).
• SVDModel now only stores U and S since V is not needed for projection.

Merged pull requests:

• Breaking changes for 0.4 - simplified IDs, support for external annotations and SCTransform update (#20) (@rasmushenningsson)