From 0f3bb059f6e1716edcc75ae8d067c7491b231e9c Mon Sep 17 00:00:00 2001 From: Oren Ben-Kiki Date: Thu, 20 Jun 2024 17:26:28 +0300 Subject: [PATCH] Add contracts. --- deps/document.jl | 2 +- docs/v0.1.0/.documenter-siteinfo.json | 2 +- docs/v0.1.0/anndata_format.html | 24 +- docs/v0.1.0/boxes.html | 102 ++- docs/v0.1.0/contracts.html | 870 ++++++++++++++++++++++++++ docs/v0.1.0/identify_genes.html | 136 +++- docs/v0.1.0/index.html | 140 ++++- docs/v0.1.0/objects.inv | Bin 459 -> 688 bytes docs/v0.1.0/search_index.js | 2 +- src/Metacells.jl | 3 + src/boxes.jl | 62 +- src/contracts.jl | 292 +++++++++ src/contracts.md | 47 ++ src/identify_genes.jl | 63 +- 14 files changed, 1635 insertions(+), 110 deletions(-) create mode 100644 docs/v0.1.0/contracts.html create mode 100644 src/contracts.jl create mode 100644 src/contracts.md diff --git a/deps/document.jl b/deps/document.jl index c2a4823..47d2d83 100644 --- a/deps/document.jl +++ b/deps/document.jl @@ -46,7 +46,7 @@ makedocs(; prettyurls = false, size_threshold_warn = 200 * 2^10, ), - pages = ["index.md", "anndata_format.md", "identify_genes.md", "boxes.md"], + pages = ["index.md", "contracts.md", "identify_genes.md", "boxes.md", "anndata_format.md"], ) if seen_problems diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json index 92ac9b8..b463918 100644 --- a/docs/v0.1.0/.documenter-siteinfo.json +++ b/docs/v0.1.0/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-17T13:39:41","documenter_version":"1.4.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T17:22:53","documenter_version":"1.4.1"}} \ No newline at end of file diff --git a/docs/v0.1.0/anndata_format.html b/docs/v0.1.0/anndata_format.html index 4e268c8..82fedd0 100644 --- a/docs/v0.1.0/anndata_format.html +++ b/docs/v0.1.0/anndata_format.html @@ -52,6 +52,18 @@ Metacells +
  • +Contracts + +
    • +
  • +Identify Genes + +
    • +
  • +Boxes + +
  • AnnData Format @@ -64,14 +76,6 @@
    • -
  • -Identify Genes - -
    • -
  • -Boxes - -
    • @@ -555,9 +559,7 @@

    @@ -265,8 +345,8 @@ 

     function identify_correlated_genes!(
     daf::DafWriter;
-    gene_fraction_regularization::AbstractFloat = 1e-5,
-    correlation_confidence::AbstractFloat = 0.9,
+    gene_fraction_regularization::AbstractFloat = 1.0e-5,
+    correlation_confidence::AbstractFloat = 0.99,
     overwrite::Bool = false,
 )::Nothing
 
@@ -295,7 +375,41 @@ 
    
 
  • Identify the genes that have at least that level of correlations in the unshuffled data.
 
    • 
 
-
    CONTRACT
+
    
+Inputs
+
+
    
+
    
+Axes
+
+
    
+
    
+gene
+ (required): Sequenced genes.
+
    
+
    
+metacell
+ (required): Minimal-sized groups of cells for robust point estimates.
+
    
+
    
+Matrices
+
+
    
+
    
+gene, metacell @ fraction
+::AbstractFloat (required): The estimated fraction of the UMIs of each gene in each metacell.
+
    
+
    
+Outputs
+
+
    
+
    
+Vectors
+
+
    
+
    
+gene @ is_correlated
+::Bool (guaranteed): A mask of genes that are correlated with other gene(s).

    @@ -336,7 +450,7 @@