-AnnData Format - - - - - -
-Metacells.AnnDataFormat
-
- —
-Module
-
-Metacells.AnnDataFormat.import_h5ads!
-
- —
-Function
-
-
-function import_h5ads!(
- destination::DafWriter;
- raw_cells_h5ad::Maybe{AbstractString} = nothing,
- clean_cells_h5ad::AbstractString,
- metacells_h5ad::AbstractString,
- copy_clean_data::Maybe{CopyAnnData} = nothing,
- type_property::Maybe{AbstractString} = nothing,
- rename_type::Maybe{AbstractString} = "type",
- type_colors_csv::Maybe{AbstractString} = nothing,
- type_properties::Maybe{AbstractSet{<:AbstractString}} = nothing,
- properties_defaults::Maybe{Dict} = nothing,
-)::Nothing
-
-
-Import an
-AnnData
-
based metacells dataset into a
-Daf
-
-destination
-
data set. Ideally, the input must include
-clean_cells_h5ad
-
and the
-metacells_h5ad
-
computed for them, and optionally also the
-raw_cells_h5ad
-
including the excluded cells and genes.
-
If type annotations were assigned to the metacells, then the name of the
-type_property
-
should be specified. This can be further enhanced by specifying a
-type_colors_csv
-
file mapping type names to colors. This should be a comma or tab separated file containing at least two columns, one named "color" and one with the same name as the
-type_property
-
. For consistency, by default the
-type_property
-
is renamed to the value of
-rename_type
-
(by default, "type"). You can disable this by setting
-rename_type
-
to
-nothing
-
. We also call
-reconstruct_axis!
-
to build the type axis; you can therefore specify an
-empty_type
-
name, which will be converted to the empty string, to match the
-Daf
-
convention of "no value" for string data, and specify an explicit set of
-type_properties
-
(by default, any per-metacell property that has the same value for all metacells of each type will be converted to a type property) and
-properties_defaults
-
.
-
This will mostly just read all the specified
-h5ad
-
files and copy the data into the
-destination
-
, with the following changes to match the
-$Daf$
- capabilities and conventions:
-
-
-
- The
-
X -
matrix of the cells is renamed to -UMIs -
, and the -X -
matrix of the metacells is renamed to -fraction -
. -
- - Matrices and vectors of counts (UMIs, zeros) or module indices are converted to an unsigned type. - -
- The
-
__name__ -
scalar is not copied. -
- - The
-
excluded_gene -
and -excluded_cell -
masks are not copied. Instead, if -raw_cells_h5ad -
is specified, an -is_excluded -
mask is created for both cells and genes, marking these that exist only in the -raw_cells_h5ad -
and not in -clean_cells_h5ad -
and -metacells_h5ad -
. -
- - The
-
full_gene_index -
is not copied. -
- - The
-
properly_sampled_gene -
mask is renamed to the per-gene -is_properly_sampled -
mask. -
- - The
-
bursty_lonely_gene -
mask is renamed to the per-gene -is_bursty_lonely -
mask. -
- - The
-
lateral_gene -
mask is renamed to the per-gene -is_lateral -
mask. -
- - The
-
noisy_gene -
mask is renamed to the per-gene -is_noisy -
mask. -
- - The
-
rare_gene -
mask is renamed to the per-gene -is_rare -
mask. -
- - The
-
rare_gene_module -
has 1 added to it (that is, "no module" is 0 in -Daf -
) and is renamed to -rare_module -
. -
- - The
-
lateral_genes_module -
has 1 added to it (that is, "no module" is 0 in -Daf -
) and is renamed to -lateral_module -
. -
- - The
-
marker_gene -
mask is renamed to the per-gene -is_marker -
mask. -
- - The
-
selected_gene -
mask is renamed to the per-gene -is_selected -
mask. -
- - The
-
ignored_gene -
mask is renamed to the per-gene -is_ignored -
mask. -
- - The
-
ignored_gene_of_<type> -
masks are converted to an -is_ignored -
mask per-gene-per-type. -
- - The
-
projected_noisy_gene -
mask is renamed to the per-gene -is_projected_noisy -
mask. -
- - The
-
atlas_gene -
, -atlas_lateral_gene -
, -atlas_noisy_gene -
, -atlas_marker_gene -
masks are renamed to the -is_atlas -
, -is_atlas_lateral -
, -is_atlas_noisy -
and -is_atlas_marker -
per-gene masks. -
- - The
-
essential_gene_of_<type> -
masks are converted to an -is_essential -
mask per-gene-per-type. -
- - The
-
atlas_essential_gene_of_<type> -
masks are converted to an -is_atlas_essential -
mask per-gene-per-type. -
- - The
-
fitted_gene_of_<type> -
masks are converted to an -is_fitted -
mask per-gene-per-type. -
- - The
-
fitted -
mask per-gene-per-metacell is renamed to -is_fitted -
. -
- - The
-
misfit -
mask per-gene-per-metacell is renamed to -is_misfit -
. -
- - The
-
essential -
mask per-gene-per-metacell is renamed to -is_essential -
. -
- - The
-
full_cell_index -
is not copied. -
- - The
-
properly_sampled_cell -
mask is renamed to the per-cell -is_properly_sampled -
mask. -
- - The
-
rare_cell -
mask is renamed to the per-cell -is_rare -
mask. -
- - The
-
cells_rare_gene_module -
has 1 added to it (that is, "no module" is 0 in -Daf -
) and is renamed to -rare_gene_module -
. -
- - The per-cell
-
dissolve -
mask is renamed to -is_dissolved -
. -
- - The per-cell
-
metacell -
integer annotation is not copied, and the -metacell_name -
string annotation is renamed to -metacell -
. -
- - The per-cell
-
most_similar -
integer annotation is not copied, and the -most_similar_name -
string annotation is renamed to -metacell.most_similar -
. -
- - The
-
rare_metacell -
mask is renamed to the per-metacell -is_rare -
mask. -
- - The per-metacell
-
metacells_level -
is renamed to -level -
. -
- - The per-metacell
-
similar -
mask is renamed to -is_similar -
. -
-
There is much duplication of data between the three
-h5ad
-
files (in particular, per-gene data). Data in
-raw_cells_h5ad
-
will override data in
-clean_cells_h5ad
-
, which will override data in
-metacells_h5ad
-
.
-
Data that exists only in
-clean_cells_h5ad
-
poses a question when being copied into the full data set, which includes the full raw set of cells and genes. If
-copy_clean_data
-
is
-nothing
-
(the default), this is simply an error. Otherwise, data that is listed in
-copy_clean_data
-
is copied using the specified name and the default value is applied to the raw-only genes or cells.
-
It is common to call
-reconstruct_axis!
-
on the result (e.g., if the cells were collected from a set of batches).
-
Metacells.AnnDataFormat.CopyAnnData
-
- —
-Type
-
-Specify how to copy data from
-AnnData
-
to
-Daf
-
. The key is simply a vector or matrix name (ignoring axes), and the value is either
-nothing
-
to ignore the data, or a tuple with the name of the destination
-Daf
-
property and an optional value to use for missing entries (raw-only cells and/or genes).
-