Struct bustools_cli::countmatrix::CountMatrix

pub struct CountMatrix {
    pub matrix: CsMat<i32>,
    /* private fields */
}

Countmatrix, cells-by-genes

Cells and genes are indexed via their string reprensentation

Fields

matrix: CsMat<i32>

sparse count matrix

Implementations

impl CountMatrix

pub fn new( matrix: CsMat<i32>, cbs: Vec<String>, genes: Vec<String> ) -> CountMatrix

create a CountMatrix from a sparse matrix type (sprs::CsMat) and name the rows (cells) and columns (genes)

pub fn get_shape(&self) -> (usize, usize)

get the matrix’s shape (nrows, ncols)

pub fn from_disk(mtx_file: &str, cbfile: &str, genefile: &str) -> Self

load a countmatrix from disk (kallisto format: mtx + barcodes.txt + genes)

pub fn from_folder(foldername: &str) -> Self

load the countmatrix from a folder, assuming standatd file naming

pub fn write(&self, foldername: &str)

write the matrix to disk in MatrixMarket format + cell and gene metadata (just like kallisto)

creates 3 files:

• gene.mtx: the sparse matrix
• gene.barcodes.txt: String representation fo the cell barcodes
• gene.genes.txt: Gene names

Trait Implementations

impl Debug for CountMatrix

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

Formats the value using the given formatter.

impl Display for CountMatrix

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

Formats the value using the given formatter.

impl PartialEq<CountMatrix> for CountMatrix

fn eq(&self, other: &Self) -> bool

comparing countmatrices. True if they represnet the same cb/gene counts irrespective of ordering

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for CountMatrix