server/queue/task/plot: Move t-SNE transformer to core

Author: zaeleus

Cargo.lock

@@ -4,6 +4,7 @@ version = "0.1.0"
 edition.workspace = true
 
 [dependencies]
+bhtsne = { version = "0.5.2", default-features = false }
 indexmap.workspace = true
 ndarray = "0.16.1"
 noodles = { workspace = true, features = ["core", "gff"] }

atlas-core/Cargo.toml

@@ -1,2 +1,3 @@
+pub mod dimension_reduction;
 pub mod normalization;
 pub mod reader;

atlas-core/src/counts.rs

@@ -0,0 +1 @@
+pub mod tsne;

atlas-core/src/counts/dimension_reduction.rs

@@ -0,0 +1,23 @@
+pub fn transform(perplexity: f64, theta: f64, counts: Vec<i32>, feature_count: usize) -> Vec<f64> {
+    fn euclidean_distance(a: &&[f64], b: &&[f64]) -> f64 {
+        a.iter()
+            .zip(b.iter())
+            .map(|(p, q)| (p - q).powi(2))
+            .sum::<f64>()
+            .sqrt()
+    }
+
+    let sum: u64 = counts.iter().map(|n| *n as u64).sum();
+
+    let normalized_counts: Vec<_> = counts
+        .into_iter()
+        .map(|count| (count as f64) / (sum as f64))
+        .collect();
+
+    let data: Vec<_> = normalized_counts.chunks(feature_count).collect();
+
+    bhtsne::tSNE::new(&data)
+        .perplexity(perplexity)
+        .barnes_hut(theta, euclidean_distance)
+        .embedding()
+}

atlas-core/src/counts/dimension_reduction/tsne.rs

@@ -7,7 +7,6 @@ edition.workspace = true
 anyhow.workspace = true
 atlas-core = { path = "../atlas-core", version = "0.1.0" }
 axum = "0.7.1"
-bhtsne = { version = "0.5.2", default-features = false }
 clap = { workspace = true, features = ["derive", "env"] }
 dotenvy = "0.15.0"
 futures = { version = "0.3.21", default-features = false, features = ["std"] }

atlas-server/Cargo.toml

@@ -3,6 +3,7 @@ mod options;
 
 use std::collections::HashMap;
 
+use atlas_core::counts::dimension_reduction::tsne;
 use sqlx::PgPool;
 
 pub use self::{error::Error, options::Options};
@@ -84,7 +85,7 @@ pub async fn plot(
         });
     }
 
-    let embedding = transform(options.perplexity, options.theta, raw_counts, feature_count);
+    let embedding = tsne::transform(options.perplexity, options.theta, raw_counts, feature_count);
 
     let mut xs = Vec::with_capacity(sample_count);
     let mut ys = Vec::with_capacity(sample_count);
@@ -103,30 +104,6 @@ fn is_perplexity_too_large(perplexity: f64, sample_count: usize) -> bool {
     sample_count > 0 && (n - 1.0 < 3.0 * perplexity)
 }
 
-fn transform(perplexity: f64, theta: f64, counts: Vec<i32>, feature_count: usize) -> Vec<f64> {
-    fn euclidean_distance(a: &&[f64], b: &&[f64]) -> f64 {
-        a.iter()
-            .zip(b.iter())
-            .map(|(p, q)| (p - q).powi(2))
-            .sum::<f64>()
-            .sqrt()
-    }
-
-    let sum: u64 = counts.iter().map(|n| *n as u64).sum();
-
-    let normalized_counts: Vec<_> = counts
-        .into_iter()
-        .map(|count| (count as f64) / (sum as f64))
-        .collect();
-
-    let data: Vec<_> = normalized_counts.chunks(feature_count).collect();
-
-    bhtsne::tSNE::new(&data)
-        .perplexity(perplexity)
-        .barnes_hut(theta, euclidean_distance)
-        .embedding()
-}
-
 #[cfg(test)]
 mod tests {
     use super::*;