rename multiomic to multilist

bzhanglab · Jan 16, 2024 · 6e960cd · 6e960cd
1 parent ee61f63
commit 6e960cd
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Showing 6 changed files with 59 additions and 42 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -2,7 +2,7 @@
 
 [package]
 name = "webgestalt"
-version = "0.1.1"
+version = "0.2.0"
 authors = ["John Elizarraras"]
 edition = "2021"
 rust-version = "1.63.0"

diff --git a/src/main.rs b/src/main.rs
@@ -5,7 +5,7 @@ use owo_colors::{OwoColorize, Stream::Stdout, Style};
 use std::io::{BufReader, Write};
 use std::{fs::File, time::Instant};
 use webgestalt_lib::methods::gsea::GSEAConfig;
-use webgestalt_lib::methods::multiomics::{combine_gmts, MultiOmicsMethod, NormalizationMethod};
+use webgestalt_lib::methods::multilist::{combine_gmts, MultiListMethod, NormalizationMethod};
 use webgestalt_lib::methods::ora::ORAConfig;
 use webgestalt_lib::readers::utils::Item;
 use webgestalt_lib::readers::{read_gmt_file, read_rank_file};
@@ -126,7 +126,7 @@ fn main() {
                     "webgestalt_lib/data/ktest.gmt".to_owned(),
                 );
                 let start = Instant::now();
-                let res = webgestalt_lib::methods::gsea::gsea(
+                let _res = webgestalt_lib::methods::gsea::gsea(
                     gene_list.unwrap(),
                     gmt.unwrap(),
                     GSEAConfig::default(),
@@ -280,13 +280,13 @@ fn main() {
                     Some(NormMethods::MedianValue) => NormalizationMethod::MedianValue,
                     None => panic!("No normalization method chosen."),
                 };
-                let method: MultiOmicsMethod = match ora_args.combination {
-                    Some(CombinationMethods::Mean) => MultiOmicsMethod::Mean(norm_method),
-                    Some(CombinationMethods::Max) => MultiOmicsMethod::Max(norm_method),
+                let method: MultiListMethod = match ora_args.combination {
+                    Some(CombinationMethods::Mean) => MultiListMethod::Mean(norm_method),
+                    Some(CombinationMethods::Max) => MultiListMethod::Max(norm_method),
                     None => panic!("No combination method chosen."),
                 };
                 let mut combined_list =
-                    webgestalt_lib::methods::multiomics::combine_lists(lists, method);
+                    webgestalt_lib::methods::multilist::combine_lists(lists, method);
                 combined_list.sort_by(|a, b| b.rank.partial_cmp(&a.rank).unwrap());
                 let mut file = File::create(ora_args.out.clone().unwrap()).unwrap();
                 println!(

diff --git a/webgestalt_lib/Cargo.toml b/webgestalt_lib/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "webgestalt_lib"
-version = "0.1.1"
+version = "0.2.0"
 authors = ["John Elizarraras"]
 edition = "2021"
 rust-version = "1.63.0"

diff --git a/webgestalt_lib/README.md b/webgestalt_lib/README.md
@@ -6,18 +6,18 @@ Library for performing different types of enrichment analyses. Serves as the und
 
 Supported methods include:
 
-- Over-representation analysis (ORA)
+- Over-Representation Analysis (ORA)
 - Gene Set Enrichment Analysis (GSEA)
 
 ## Installation
 
 To use webgestalt_lib in your Rust project, add the following line to your `Cargo.toml`.
 
 ```toml
-webgestalt_lib = "0.1.0" # change to wanted version
+webgestalt_lib = "0.1.1" # change to wanted version
 ```
 
-If you are just interested in running an analysis, rather than develop new tools, please use on of the packages mentioned at the beginning of the README.
+If you are just interested in running an analysis, rather than develop new tools, please use one of the packages mentioned at the beginning of the README.
 
 ## Development Priorities
 
@@ -27,7 +27,7 @@ If you are just interested in running an analysis, rather than develop new tools
 3. Fast compilation times
    - Every package install has to build the library from scratch, so the lower number of dependencies, the better
 
-This crate does not provide any data formatting, or charts to display the results of the analysis. This work has already been done by the [R package](https://github.com/bzhanglab/webgestaltr), and a limited implementation is provided by the Rust CLI. The focus for this library is purely computational.
+This crate does not provide any data formatting or charts to display the results of the analysis. This work has already been done by the [R package](https://github.com/bzhanglab/webgestaltr), and a limited implementation is provided by the Rust CLI. The focus for this library is purely computational.
 
 ## License
 

diff --git a/webgestalt_lib/src/methods.rs b/webgestalt_lib/src/methods.rs
@@ -1,3 +1,3 @@
 pub mod gsea;
-pub mod multiomics;
+pub mod multilist;
 pub mod ora;
diff --git a/webgestalt_lib/src/methods/multiomics.rs → webgestalt_lib/src/methods/multilist.rs b/webgestalt_lib/src/methods/multiomics.rs → webgestalt_lib/src/methods/multilist.rs
@@ -5,9 +5,13 @@ use super::{
     gsea::{GSEAConfig, GSEAResult, RankListItem},
     ora::{get_ora, ORAConfig, ORAResult},
 };
-use crate::{methods::gsea::gsea, readers::utils::Item};
+use crate::{
+    methods::gsea::gsea,
+    readers::utils::Item,
+    stat::{adjust, AdjustmentMethod},
+};
 
-pub enum MultiOmicsMethod {
+pub enum MultiListMethod {
     /// Get the max median ratio of the analyte from any list
     Max(NormalizationMethod),
     /// Get the average median ratio of analyte from all the lists
@@ -49,7 +53,7 @@ pub enum NormalizationMethod {
     None,
 }
 
-/// Run a multiomics analysis, using either the max/mean median ratio or a typical meta analysis
+/// Run a multilist analysis, using either the max/mean median ratio or a typical meta analysis
 /// method
 ///
 /// # Parameters
@@ -61,8 +65,8 @@ pub enum NormalizationMethod {
 ///
 /// Returns a [`Vec<Vec<FullGSEAResult>>`] containing the results of each analysis. If the method was not meta-analysis, then the outer vector will only have one element.
 /// If the method was meta-analysis, then the first element will be the results of the meta-analysis, and the rest of the elements will be the results of each analysis run individually.
-pub fn multiomic_gsea(jobs: Vec<GSEAJob>, method: MultiOmicsMethod) -> Vec<Vec<GSEAResult>> {
-    if let MultiOmicsMethod::Meta(meta_method) = method {
+pub fn multilist_gsea(jobs: Vec<GSEAJob>, method: MultiListMethod) -> Vec<Vec<GSEAResult>> {
+    if let MultiListMethod::Meta(meta_method) = method {
         let mut phash: AHashMap<String, Vec<f64>> = AHashMap::default();
         let mut results: Vec<Vec<GSEAResult>> = Vec::new();
         for job in jobs {
@@ -119,9 +123,24 @@ pub fn multiomic_gsea(jobs: Vec<GSEAJob>, method: MultiOmicsMethod) -> Vec<Vec<G
     }
 }
 
-pub fn multiomic_ora(jobs: Vec<ORAJob>, method: MultiOmicsMethod) -> Vec<Vec<ORAResult>> {
+/// Perform multi-list over-representation analysis
+///
+/// # Parameters
+///
+/// - `jobs` - [`Vec<ORAJob>`] containing [`ORAJob`] for each list
+/// - `method` - [`MultiListMethod`] detailing how to combine the different lists (i.e. meta-analysis)
+/// - `fdr_method` - [`AdjustmentMethod`] of what FDR method to use to adjust p-values
+///
+/// # Panics
+///
+/// Panics if there is a arithmetic error.
+pub fn multilist_ora(
+    jobs: Vec<ORAJob>,
+    method: MultiListMethod,
+    fdr_method: AdjustmentMethod,
+) -> Vec<Vec<ORAResult>> {
     match method {
-        MultiOmicsMethod::Meta(meta_method) => {
+        MultiListMethod::Meta(meta_method) => {
             let mut phash: AHashMap<String, Vec<f64>> = AHashMap::default();
             let mut results: Vec<Vec<ORAResult>> = Vec::new();
             for job in jobs {
@@ -133,33 +152,31 @@ pub fn multiomic_ora(jobs: Vec<ORAJob>, method: MultiOmicsMethod) -> Vec<Vec<ORA
                 results.push(res);
             }
             let mut final_result: Vec<ORAResult> = Vec::new();
+            let mut meta_p = Vec::new();
             match meta_method {
                 MetaAnalysisMethod::Stouffer => {
                     let normal = Normal::new(0.0, 1.0).unwrap();
                     for set in phash.keys() {
-                        final_result.push(ORAResult {
-                            set: set.clone(),
-                            p: stouffer_with_normal(&phash[set], &normal),
-                            fdr: 0.0,
-                            overlap: 0,
-                            expected: 0.0,
-                            enrichment_ratio: 0.0,
-                        });
+                        meta_p.push(stouffer_with_normal(&phash[set], &normal))
                     }
                 }
                 MetaAnalysisMethod::Fisher => {
                     for set in phash.keys() {
-                        final_result.push(ORAResult {
-                            set: set.clone(),
-                            p: fisher(&phash[set]),
-                            fdr: 0.0,
-                            overlap: 0,
-                            expected: 0.0,
-                            enrichment_ratio: 0.0,
-                        });
+                        meta_p.push(fisher(&phash[set]));
                     }
                 }
             }
+            let meta_fdr = adjust(&meta_p, fdr_method);
+            for (i, set) in phash.keys().enumerate() {
+                final_result.push(ORAResult {
+                    set: set.clone(),
+                    p: meta_p[i],
+                    fdr: meta_fdr[i],
+                    overlap: 0,
+                    expected: 0.0,
+                    enrichment_ratio: 0.0,
+                })
+            }
             results.insert(0, final_result);
             results
         }
@@ -171,12 +188,12 @@ pub fn multiomic_ora(jobs: Vec<ORAJob>, method: MultiOmicsMethod) -> Vec<Vec<ORA
 
 pub fn combine_lists(
     lists: Vec<Vec<RankListItem>>,
-    combination_method: MultiOmicsMethod,
+    combination_method: MultiListMethod,
 ) -> Vec<RankListItem> {
     match combination_method {
-        MultiOmicsMethod::Max(normalization_method) => max_combine(lists, normalization_method),
-        MultiOmicsMethod::Mean(normalization_method) => mean_combine(lists, normalization_method),
-        MultiOmicsMethod::Meta(_) => panic!("Lists can not be combined for meta-analysis"),
+        MultiListMethod::Max(normalization_method) => max_combine(lists, normalization_method),
+        MultiListMethod::Mean(normalization_method) => mean_combine(lists, normalization_method),
+        MultiListMethod::Meta(_) => panic!("Lists can not be combined for meta-analysis"),
     }
 }
 
@@ -333,7 +350,7 @@ pub fn combine_gmts(gmts: &Vec<Vec<Item>>) -> Vec<Item> {
 /// # Examples
 ///
 /// ```rust
-/// use webgestalt_lib::methods::multiomics::stouffer;
+/// use webgestalt_lib::methods::multilist::stouffer;
 /// let vals: Vec<f64> = vec![0.1, 0.01, 0.11, 0.23];
 /// let metap: f64 = stouffer(&vals);
 /// ```
@@ -363,7 +380,7 @@ pub fn fisher(vals: &Vec<f64>) -> f64 {
 /// # Examples
 ///
 /// ```rust
-/// use webgestalt_lib::methods::multiomics::stouffer_weighted;
+/// use webgestalt_lib::methods::multilist::stouffer_weighted;
 /// let vals: Vec<f64> = vec![0.1, 0.01, 0.11, 0.23];
 /// let weights: Vec<f64> = vec![0.1, 0.2, 0.3, 0.4];
 /// let metap: f64 = stouffer_weighted(vals, weights);