up

src/lib.rs

@@ -365,8 +365,8 @@ mod tests {
 
     #[test]
     fn gene_translocations() -> anyhow::Result<()> {
-        let gene_name = "NOTCH1";
-        let translocs = read_translocs("/data/tmp_trl.tsv")?;
+        let gene_name = "TLX1";
+        let translocs = read_translocs("/data/tlx1_translocations.tsv")?;
 
         // Select translocations having one partner with gene_name
         let translocs: Vec<TranslocData> = translocs
@@ -841,9 +841,9 @@ mod tests {
 
     #[test]
     fn lol() -> anyhow::Result<()> {
-        let id = "NM_017617.5"; // NOTCH1
+        // let id = "NM_017617.5"; // NOTCH1
                                 // let id = "NM_000314.8"; // PTEN
-                                // let id = "NM_001015877.2"; // PHF6
+                                let id = "NM_001015877.2"; // PHF6
                                 // let id = "NM_001005361.3"; // DNM2
                                 // let id = "NM_002185.5"; // IL7R
         let pten_cfg = loliplot::SvgConfig {
@@ -933,4 +933,83 @@ mod tests {
 
         Ok(())
     }
+
+    #[test]
+    fn hoxa_translocations() -> anyhow::Result<()> {
+        let translocs = read_translocs("/data/hoxa_translocations.tsv")?;
+
+        // Chromosomes to render
+        let mut chroms: Vec<String> = Vec::new();
+        for chr_id in 0..24 {
+            let chr_name = if chr_id <= 21 {
+                format!("chr{}", chr_id + 1)
+            } else if chr_id == 22 {
+                "chrX".to_string()
+            } else {
+                "chrY".to_string()
+            };
+
+            let present = translocs
+                .iter()
+                .any(|t| t.left_chr == chr_name || t.right_chr == chr_name);
+            if present && !chroms.contains(&chr_name) {
+                chroms.push(chr_name);
+            }
+        }
+
+        let cfg = circ::CircosConfig {
+            r: 300.0,
+            ..Default::default()
+        };
+
+        let mut circos = circ::Circos::new_with_chrom(&chroms, cfg)?;
+
+        // LABELS
+        let mut hm: HashMap<String, (usize, u32, usize)> = HashMap::new();
+
+        translocs.iter().for_each(|t| {
+            let left_chrom_id = *circos.chroms_ids.get(&t.left_chr).unwrap();
+            hm.entry(t.left_gene.to_string())
+                .and_modify(|e| e.2 += 1)
+                .or_insert((left_chrom_id, t.left_pos, 1));
+
+            let right_chrom_id = *circos.chroms_ids.get(&t.right_chr).unwrap();
+            hm.entry(t.right_gene.to_string())
+                .and_modify(|e| e.2 += 1)
+                .or_insert((right_chrom_id, t.right_pos, 1));
+        });
+        circos.add_labels(
+            &hm.iter()
+                .map(|(gene, (id, pos, n))| (format!("{gene} (n={n})"), *id, *pos))
+                .collect::<Vec<(String, usize, u32)>>(),
+        );
+
+        // ARCS
+        translocs.iter().for_each(|t| {
+            let left_chrom_id = *circos.chroms_ids.get(&t.left_chr).unwrap();
+            let right_chrom_id = *circos.chroms_ids.get(&t.right_chr).unwrap();
+            circos.tracks[circos.ref_track.unwrap()].add_cord(
+                circ::Attach::Data {
+                    set_idx: left_chrom_id,
+                    start: t.left_pos,
+                    end: None,
+                },
+                circ::Attach::Data {
+                    set_idx: right_chrom_id,
+                    start: t.right_pos,
+                    end: None,
+                },
+                circos.config.r - (circos.config.r * 0.1),
+                0.3,
+                "red".to_string(),
+                2,
+            );
+        });
+
+        circos.save_to_file(
+            &format!("/data/genes_results/HOXA_translocations.svg"),
+            100.0,
+        )?;
+        Ok(())
+    }
 }