Struct MatrixLayout 

pub struct MatrixLayout {
    pub data_field: Box<str>,
    pub indices_field: Box<str>,
    pub indptr_field: Box<str>,
    pub pointer_type: IndexPointerType,
    pub row_id_field: Box<str>,
    pub row_name_field: Box<str>,
    pub row_type_field: Box<str>,
    pub select_row_type: Box<str>,
    pub remove_row_type: Box<str>,
    pub column_name_field: Box<str>,
}

Where a 10x file keeps its sparse matrix and the names of its rows and columns, and which rows to keep: MatrixLayout::cell_ranger_h5 and MatrixLayout::xenium_zarr.

Fields

data_field: Box<str>

indices_field: Box<str>

indptr_field: Box<str>

pointer_type: IndexPointerType

row_id_field: Box<str>

row_name_field: Box<str>

row_type_field: Box<str>

select_row_type: Box<str>

Comma-separated, case-insensitive; a row whose type contains any is kept.

remove_row_type: Box<str>

Comma-separated, case-insensitive; a row whose type contains any is dropped.

column_name_field: Box<str>

Implementations

impl MatrixLayout

pub const H5_ROOT: &'static str = "matrix"

The group a Cell Ranger HDF5 file keeps its matrix under; the H5_* fields are relative to it.

pub const H5_DATA: &'static str = "data"

pub const H5_INDICES: &'static str = "indices"

pub const H5_INDPTR: &'static str = "indptr"

pub const H5_ROW_IDS: &'static str = "features/id"

pub const H5_ROW_NAMES: &'static str = "features/name"

pub const H5_ROW_TYPES: &'static str = "features/feature_type"

pub const H5_COLUMN_NAMES: &'static str = "barcodes"

pub const XENIUM_DATA: &'static str = "/cell_features/data"

pub const XENIUM_INDICES: &'static str = "/cell_features/indices"

pub const XENIUM_INDPTR: &'static str = "/cell_features/indptr"

pub const XENIUM_ROW_IDS: &'static str = "/cell_features/feature_ids"

pub const XENIUM_ROW_NAMES: &'static str = "/cell_features/feature_keys"

pub const XENIUM_ROW_TYPES: &'static str = "/cell_features/feature_types"

pub const XENIUM_COLUMN_NAMES: &'static str = "/cell_features/cell_id"

pub const SELECT_ROW_TYPES: &'static str = "gene,peak"

Gene Expression (Xenium gene) and ATAC Peaks.

pub const REMOVE_ROW_TYPES: &'static str = "aggregate"

Xenium’s per-gene aggregates (aggregate_gene).

pub fn cell_ranger_h5() -> Self

Cell Ranger / Space Ranger / Xenium *feature_bc_matrix.h5: features × barcodes under Self::H5_ROOT, pointers over barcodes.

pub fn xenium_zarr() -> Self

Xenium’s cell_feature_matrix.zarr: features × cells, pointers over features, feature names as attributes of /cell_features.

Trait Implementations

impl Clone for MatrixLayout

fn clone(&self) -> Self

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for MatrixLayout

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.