diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json index b463918..d638b2d 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":"2024-06-20T17:22:53","documenter_version":"1.4.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T17:56:23","documenter_version":"1.4.1"}} \ No newline at end of file diff --git a/docs/v0.1.0/boxes.html b/docs/v0.1.0/boxes.html index ee40392..646eb3f 100644 --- a/docs/v0.1.0/boxes.html +++ b/docs/v0.1.0/boxes.html @@ -249,7 +249,7 @@

metacell @ total_UMIs -::AbstractFloat (required): The total number of UMIs used to estimate the fraction of all the genes in each metacell. +::Unsigned (required): The total number of UMIs used to estimate the fraction of all the genes in each metacell.

Matrices @@ -261,7 +261,7 @@

gene, metacell @ total_UMIs -::AbstractFloat (required): The total number of UMIs used to estimate the fraction of each gene in each metacell. +::Unsigned (required): The total number of UMIs used to estimate the fraction of each gene in each metacell.

Outputs @@ -285,11 +285,11 @@

metacell @ box -::AbstractFloat (guaranteed): The unique box each metacell belongs to. +::AbstractString (guaranteed): The unique box each metacell belongs to.

box @ neighborhood.main -::AbstractFloat (guaranteed): The unique main neighborhood of each box. +::AbstractString (guaranteed): The unique main neighborhood of each box.

neighborhood @ span @@ -301,7 +301,7 @@

gene, neighborhood @ is_correlated -::AbstractFloat (guaranteed): Which genes are correlated in each neighborhood. +::Bool (guaranteed): Which genes are correlated in each neighborhood.

box, box @ distance @@ -309,7 +309,7 @@

box, neighborhood @ is_member -::AbstractFloat (guaranteed): A mask of the member boxes of each neighborhood. +::Bool (guaranteed): A mask of the member boxes of each neighborhood.

diff --git a/docs/v0.1.0/contracts.html b/docs/v0.1.0/contracts.html index 5153031..211e422 100644 --- a/docs/v0.1.0/contracts.html +++ b/docs/v0.1.0/contracts.html @@ -514,6 +514,28 @@

+ +Metacells.Contracts.metacell_type_vector + + — +Function + +
+
+
+
+function metacell_type_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
+
+
+

The type each metacell belongs to. +

+
+
+ +
+
+ + Metacells.Contracts.box_main_neighborhood_vector @@ -536,6 +558,50 @@

+ +Metacells.Contracts.box_total_UMIs_vector + + — +Function + +
+
+
+
+function box_total_UMIs_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
+
+
+

The unique main neighborhood of each box. Ideally, each box is the center of its own main neighborhood, and also belongs to overlapping neighborhood of some other nearby boxes. However, where the manifold is sparsely sampled, a few nearby boxes may share the same main neighborhood. If the samples are sufficiently sparse, the main neighborhood may include only just the single box (which itself may include just a single metacell). +

+
+
+

+
+
+ + + +Metacells.Contracts.box_type_vector + + — +Function + +
+
+
+
+function box_type_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
+
+
+

The type each box belongs to. +

+
+
+
+
+
+ + Metacells.Contracts.neighborhood_span_vector @@ -554,6 +620,28 @@

+
+
+ + + +Metacells.Contracts.type_color_vector + + — +Function + +
+
+
+
+function type_color_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
+
+
+

A unique color for each type for graphs. +

+
+
+

Matrices @@ -654,6 +742,50 @@

+ +Metacells.Contracts.gene_box_fraction_matrix + + — +Function + +
+
+
+
+function gene_box_fraction_matrix(expectation::ContractExpectation)::Pair{MatrixKey, DataSpecification}
+
+
+

The estimated fraction of the UMIs of each gene in each box. Each box is a sample of the manifold, representing a real biological state, which is different from the state of any other box. +

+
+
+ +
+
+ + + +Metacells.Contracts.gene_box_total_UMIs_matrix + + — +Function + +
+
+
+
+function gene_box_total_UMIs_matrix(expectation::ContractExpectation)::Pair{MatrixKey, DataSpecification}
+
+
+

The total number of UMIs used to estimate the fraction of each gene in each box. This is used to estimate the robustness of the estimate. When computing fold factors, we require the total number of UMIs (from both compared estimates) to be some minimum, and possibly adjust the fold factor according to some confidence level (assuming a multinomial sampling distribution). +

+
+
+
+
+
+ + Metacells.Contracts.box_neighborhood_is_member_matrix @@ -712,6 +844,18 @@

  • + +Metacells.Contracts.box_total_UMIs_vector + + +
  • +
  • + +Metacells.Contracts.box_type_vector + + +
  • +
  • Metacells.Contracts.cell_axis @@ -730,6 +874,18 @@

  • + +Metacells.Contracts.gene_box_fraction_matrix + + +
  • +
  • + +Metacells.Contracts.gene_box_total_UMIs_matrix + + +
  • +
  • Metacells.Contracts.gene_divergence_vector @@ -796,6 +952,12 @@

  • + +Metacells.Contracts.metacell_type_vector + + +
  • +
  • Metacells.Contracts.neighborhood_axis @@ -813,6 +975,12 @@

  • +
  • + +Metacells.Contracts.type_color_vector + + +