Struct ExpressionMatrix 

pub struct ExpressionMatrix { /* private fields */ }

A dense, row-major expression matrix (features × samples).

Implementations

impl ExpressionMatrix

pub fn new( data: Vec<Vec<f64>>, feature_names: Vec<String>, sample_names: Vec<String>, ) -> Result<Self>

Create a matrix from row-major 2D data.

Each inner Vec is one feature (row) with n_samples values.

pub fn zeros( n_features: usize, n_samples: usize, feature_names: Vec<String>, sample_names: Vec<String>, ) -> Result<Self>

Create a zero-filled matrix.

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

(n_features, n_samples).

pub fn get(&self, feature_idx: usize, sample_idx: usize) -> Option<f64>

Get a single value by feature and sample index.

pub fn set( &mut self, feature_idx: usize, sample_idx: usize, value: f64, ) -> Result<()>

Set a single value. Returns an error if indices are out of bounds.

pub fn row(&self, feature_idx: usize) -> Option<&[f64]>

A slice of one feature’s expression across all samples.

pub fn column(&self, sample_idx: usize) -> Option<Vec<f64>>

All feature values for a single sample (column copy, since data is row-major).

pub fn row_mean(&self, feature_idx: usize) -> Option<f64>

Mean expression of a feature across all samples.

pub fn column_mean(&self, sample_idx: usize) -> Option<f64>

Mean expression across all features for a sample.

pub fn transpose(&self) -> ExpressionMatrix

Transpose the matrix, swapping features and samples.

pub fn filter_features(&self, indices: &[usize]) -> Result<ExpressionMatrix>

Subset the matrix to the given feature (row) indices.

pub fn filter_samples(&self, indices: &[usize]) -> Result<ExpressionMatrix>

Subset the matrix to the given sample (column) indices.

pub fn as_slice(&self) -> &[f64]

The underlying flat data as a slice (row-major, n_features × n_samples).

pub fn feature_names(&self) -> &[String]

Feature (gene/protein) names.

pub fn sample_names(&self) -> &[String]

Sample names.

pub fn log_transform(&self, pseudocount: f64) -> ExpressionMatrix

Log2-transform all values: log2(x + pseudocount).

Commonly used to normalize RNA-seq count data.

Trait Implementations

impl Clone for ExpressionMatrix

fn clone(&self) -> ExpressionMatrix

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ExpressionMatrix

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

Formats the value using the given formatter.

impl Summarizable for ExpressionMatrix

fn summary(&self) -> String

A one-line summary suitable for display.