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16 run pseudo rank tests in parallel #17

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merged 2 commits into from
May 19, 2023
Merged

16 run pseudo rank tests in parallel #17

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cd30b7e
allow rank test in parallel with rayon
noamteyssier May 19, 2023
6d996fa
added rayon as feature to ndarray + bump version
noamteyssier May 19, 2023
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4 changes: 2 additions & 2 deletions Cargo.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[package]
name = "intc"
version = "0.3.0"
version = "0.3.1"
edition = "2021"
description = "An implementation of the *-INC method to calculate an empirical FDR for non-targeting controls in CRISPR screens "
license = "MIT"
Expand All @@ -14,6 +14,6 @@ categories = ["science"]
[dependencies]
anyhow = "1.0.68"
hashbrown = "0.13.2"
ndarray = "0.15.6"
ndarray = { version = "0.15.6", features = ["rayon"] }
ndarray-rand = "0.14.0"
statrs = "0.16.0"
26 changes: 13 additions & 13 deletions src/rank_test.rs
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Expand Up @@ -2,7 +2,7 @@ use crate::{
mwu::{mann_whitney_u, Alternative},
utils::select_values,
};
use ndarray::{s, Array1, Array2, Axis};
use ndarray::{Array1, Array2, Axis, Zip};
use ndarray_rand::{
rand::{rngs::StdRng, SeedableRng},
rand_distr::Uniform,
Expand Down Expand Up @@ -78,27 +78,27 @@ pub fn pseudo_rank_test_matrix(
) -> (Array2<f64>, Array2<f64>) {
let mut pseudo_pvalues = Array2::zeros((n_tests, n_genes));
let mut pseudo_logfc = Array2::zeros((n_tests, n_genes));
let binding = Array1::range(0.0, n_tests as f64, 1.0)
.insert_axis(Axis(1));
let array_idx = binding
.broadcast((n_tests, 1))
.unwrap();

(0..n_tests)
.map(|idx| {
Zip::from(pseudo_pvalues.rows_mut())
.and(pseudo_logfc.rows_mut())
.and(array_idx.rows())
.par_for_each(|mut pvalues, mut logfcs, idx| {
let (pseudo_pvalues, pseudo_logfcs) = pseudo_rank_test(
n_genes,
s_pseudo,
ntc_pvalues,
ntc_logfcs,
alternative,
continuity,
seed + idx as u64,
seed + idx[0] as u64,
);
(idx, pseudo_pvalues, pseudo_logfcs)
})
.for_each(|(idx, pvalues, logfcs)| {
pseudo_logfc
.slice_mut(s![idx, ..])
.zip_mut_with(&logfcs, |x, &y| *x += y);
pseudo_pvalues
.slice_mut(s![idx, ..])
.zip_mut_with(&pvalues, |x, &y| *x += y);
pvalues += &pseudo_pvalues;
logfcs += &pseudo_logfcs;
});

(pseudo_pvalues, pseudo_logfc)
Expand Down