Merge pull request YangLab-um#22 from ftavella/update-network-utilities

Update network utilities and input handling - New functionality

src/BiologicalOscillations.jl

@@ -18,8 +18,13 @@ export pin_hit_rate
 export gene_regulatory_network, grn_parameters, grn_timescale, grn_parameter_sets
 export grn_equilibration_times, find_grn_oscillations
 # Network utilities
-export network_permutations, is_same_network, is_directed_cycle_graph, is_same_set_of_networks, all_network_additions, unique_network_additions, unique_negative_feedback_networks, unique_cycle_addition
+export network_permutations, is_same_network, all_network_additions, unique_network_additions
+export is_directed_cycle_graph, is_same_set_of_networks, unique_cycle_addition
+export unique_negative_feedback_networks, count_inputs_by_coherence, is_negative_feedback_network
 export connectivity_to_binary, find_all_binary_circular_permutations, binary_to_connectivity
+export calculate_node_coherence
+# User input handling
+export is_valid_connectivity, connectivity_string_to_matrix
 # Default hyperparameters
 export DEFAULT_PIN_HYPERPARAMETERS, DEFAULT_PIN_PARAMETER_LIMITS, DEFAULT_PIN_SAMPLING_SCALES
 export DEFAULT_GRN_HYPERPARAMETERS, DEFAULT_GRN_PARAMETER_LIMITS, DEFAULT_GRN_SAMPLING_SCALES

src/network_utilities.jl

@@ -40,6 +40,13 @@ end
 - `result::Bool`: True if any of the permutations of connectivity 1 is equal to any of the permutations of connectivity2. False otherwise.
 """
 function is_same_network(connectivity1::AbstractMatrix, connectivity2::AbstractMatrix)
+    if connectivity1 == connectivity2
+        return true
+    end
+    # If the sum of edges is different, then the networks are different
+    if sum(connectivity1) != sum(connectivity2)
+        return false
+    end
     permutations1 = network_permutations(connectivity1)
     permutations2 = network_permutations(connectivity2)
     # Compare permutations
@@ -165,7 +172,8 @@ function unique_network_additions(connectivity::AbstractMatrix, number_of_edges:
     all_additions = all_network_additions(connectivity, number_of_edges)
     # Remove duplicates
     for addition in all_additions
-        if !any(is_same_network(addition, c) for c in connectivity_vector)
+        comparison = [is_same_network(addition, c) for c in connectivity_vector]
+        if !any(comparison)
             push!(connectivity_vector, addition)
         end
     end
@@ -227,6 +235,33 @@ end
 
 
 """
+    count_inputs_by_coherence(connectivity::AbstractMatrix)
+
+    Returns the total number of coherent and incoherent inputs for a given network.
+
+# Arguments (Required)
+- `connectivity::AbstractMatrix`: Connectivity matrix of a network
+
+# Returns
+- `input_counts::DataFrame`: DataFrame containing the number of coherent and incoherent inputs for a given network
+"""
+function count_inputs_by_coherence(connectivity::AbstractMatrix)
+    # Initialize dataframe
+    input_counts = DataFrame(coherent = 0, incoherent = 0)
+    # Go through each row
+    for row in eachrow(connectivity)
+        node_coherence = calculate_node_coherence(row)
+        if node_coherence == "coherent"
+            input_counts.coherent .+= 1
+        elseif node_coherence == "incoherent"
+            input_counts.incoherent .+= 1
+        end
+    end
+    return input_counts
+end
+
+
+ """
    connectivity_to_binary(connectivity::AbstractMatrix)
 
    Returns a binary representation of a circular network.
@@ -273,6 +308,30 @@ end
 
 
 """
+    is_negative_feedback_network(connectivity::AbstractMatrix)
+
+    Returns true if the network is a negative-feedback-only network. False otherwise.
+
+# Arguments (Required)
+- `connectivity::AbstractMatrix`: Connectivity matrix of a network
+
+# Returns
+- `result::Bool`: True if the network is a negative-feedback-only network. False otherwise.
+"""
+function is_negative_feedback_network(connectivity::AbstractMatrix)
+    non_zero_edges = connectivity[connectivity .!= 0]
+    # If the number of edges is larger than the number of nodes, then it is not a negative-feedback-only network
+    if sum(abs.(non_zero_edges)) > size(connectivity, 1)
+        return false
+    # If the product of the edges is non-negative, then it is not a negative-feedback-only network
+    elseif prod(non_zero_edges) >= 0
+        return false
+    else
+        return true
+    end
+end
+
+ """
    find_all_binary_circular_permutations(feedback_loop_in_binary::String)
 
    Returns a vector containing all unique circular permutations of a given binary representation.
@@ -312,6 +371,33 @@ function binary_to_connectivity(feedback_loop_in_binary::String)
 end
 
 
+"""
+    calculate_node_coherence(node_inputs::AbstractVector)
+
+    Returns the coherence of a node given its inputs. A coherent node has all inputs with the same sign. An incoherent node has at least one input with a different sign.
+
+# Arguments (Required)
+- `node_inputs::AbstractVector`: Vector containing the inputs of a node
+
+# Returns
+- `coherence::String`: Coherence of a node. Either "coherent", "incoherent" or "unknown"
+"""
+function calculate_node_coherence(node_inputs::AbstractArray)
+    coherence = "unknown"
+
+    n_positive = sum(node_inputs .== 1)
+    n_negative = sum(node_inputs .== -1)
+
+    if n_positive == 0 && n_negative > 1 || n_positive > 1 && n_negative == 0
+        coherence = "coherent"
+    elseif n_positive > 0 && n_negative > 0
+        coherence = "incoherent"
+    end
+
+    return coherence
+end
+
+
 """
    unique_cycle_addition(connectivity::AbstractMatrix)
 
@@ -344,4 +430,4 @@ function unique_cycle_addition(connectivity::AbstractMatrix)
     end
 
     return connectivity_vector
-end
+end

src/user_input_handling.jl

@@ -3,7 +3,7 @@
 
 Check if connectivity is a 2-dimensional square matrix filled with 0, 1, and -1 values.
 
-# Arguments
+# Arguments (Required)
 - `connectivity::AbstractMatrix`: A matrix.
 
 # Returns
@@ -25,4 +25,25 @@ function is_valid_connectivity(connectivity::AbstractMatrix)
         result = true
     end
     return [result, errmsg]
+end
+
+
+"""
+        connectivity_string_to_matrix(connectivity_string::AbstractString)
+
+    Convert connectivity string to a 2-dimensional square matrix filled with 0, 1, and -1 values.
+
+# Arguments (Required)
+- `connectivity_string::AbstractString`: A string representing a connectivity matrix.
+
+# Returns
+- `AbstractMatrix`: A 2-dimensional square matrix filled with 0, 1, and -1 values.
+"""
+function connectivity_string_to_matrix(connectivity_string::AbstractString)
+    connectivity_values = replace(connectivity_string, ";" => "", "[" => "", "]" => "")
+    connectivity_array = [parse(Int, i) for i in split(connectivity_values)]
+    nodes = convert(Int64, sqrt(length(connectivity_array)))
+    connectivity_array = reshape(connectivity_array, nodes, nodes)
+    connectivity_array = connectivity_array'
+    return connectivity_array
 end

test/network_utilities_tests.jl

@@ -1,6 +1,14 @@
 using BiologicalOscillations
 
-# Test that the correct network permutations are generated
+# Test `network_permutations`
+## 2 nodes
+true_permutations = [
+    [0 1; 2 0],
+    [0 2; 1 0],
+]
+calculated_permutations = network_permutations([0 1; 2 0])
+@test true_permutations == calculated_permutations
+## 3 nodes
 true_permutations = [
     [0 0 1; 2 0 0; 0 3 0],
     [0 1 0; 0 0 3; 2 0 0],
@@ -105,6 +113,104 @@ for network in true_unique_6_nodes
     @test any([is_same_network(network, calculated_network) for calculated_network in calculated_unique_6_nodes])
 end
 
+# Test the count_inputs_by_coherence function
+connectivity = [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 -1 0 0 0 0; 0 0 -1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 -1 0]
+input_counts = count_inputs_by_coherence(connectivity)
+@test input_counts.coherent[1] == 0
+@test input_counts.incoherent[1] == 0
+
+connectivity = [0 1 1;1 0 0;0 -1 1]
+input_counts = count_inputs_by_coherence(connectivity)
+@test input_counts.coherent[1] == 1
+@test input_counts.incoherent[1] == 1
+
+connectivity = [-1 1 1;1 1 1;-1 1 1]
+input_counts = count_inputs_by_coherence(connectivity)
+@test input_counts.coherent[1] == 1
+@test input_counts.incoherent[1] == 2
+
+# Test is_negative_feedback_network
+nf_networks = [
+    [0 0 -1; -1 0 0; 0 -1 0],
+    [0 0 1; 1 0 0; 0 -1 0],
+    [0 0 0 -1; 1 0 0 0; 0 -1 0 0; 0 0 -1 0],
+    [0 0 0 -1; 1 0 0 0; 0 1 0 0; 0 0 1 0],
+    [0 0 0 0 -1; -1 0 0 0 0; 0 -1 0 0 0; 0 0 -1 0 0; 0 0 0 -1 0],
+    [0 0 0 0 -1; 1 0 0 0 0; 0 1 0 0 0; 0 0 -1 0 0; 0 0 0 -1 0],
+    [0 0 0 0 -1; 1 0 0 0 0; 0 -1 0 0 0; 0 0 1 0 0; 0 0 0 -1 0],
+    [0 0 0 0 -1; 1 0 0 0 0; 0 1 0 0 0; 0 0 1 0 0; 0 0 0 1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 -1 0 0 0 0; 0 0 -1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 -1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 0 0 0; 0 0 1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 -1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 0 0 0; 0 0 -1 0 0 0; 0 0 0 1 0 0; 0 0 0 0 -1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 0 0 0; 0 0 -1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 -1 0 0 0 0; 0 0 1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 0 0 0; 0 0 1 0 0 0; 0 0 0 1 0 0; 0 0 0 0 1 0],
+    [0 0 0 0 0 0 -1; -1 0 0 0 0 0 0; 0 -1 0 0 0 0 0; 0 0 -1 0 0 0 0; 0 0 0 -1 0 0 0; 0 0 0 0 -1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 1 0 0 0 0 0; 0 0 -1 0 0 0 0; 0 0 0 -1 0 0 0; 0 0 0 0 -1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 -1 0 0 0 0 0; 0 0 1 0 0 0 0; 0 0 0 -1 0 0 0; 0 0 0 0 -1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 -1 0 0 0 0 0; 0 0 -1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 -1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 1 0 0 0 0 0; 0 0 1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 -1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 -1 0 0 0 0 0; 0 0 1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 -1 0 0 0 0 0; 0 0 -1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 1 0 0; 0 0 0 0 0 1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 1 0 0 0 0 0; 0 0 -1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 1 0 0; 0 0 0 0 0 -1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 1 0 0 0 0 0; 0 0 -1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 -1 0 0; 0 0 0 0 0 1 0],
+    [0 0 0 0 0 0 -1; 1 0 0 0 0 0 0; 0 1 0 0 0 0 0; 0 0 1 0 0 0 0; 0 0 0 1 0 0 0; 0 0 0 0 1 0 0; 0 0 0 0 0 1 0],
+]
+
+non_nf_networks = [
+    [0 0 1; -1 0 0; 0 -1 0],
+    [0 0 1; 1 0 0; 0 1 0],
+    [0 0 0 -1; 1 0 0 1; 0 -1 0 0; 0 0 -1 0],
+    [0 0 0 -1; 1 0 1 0; 1 1 0 0; 0 0 1 0],
+    [0 0 0 0 -1; -1 0 0 0 0; 0 0 0 0 0; 0 0 -1 0 0; 0 0 0 -1 0],
+    [0 0 0 0 -1; 1 0 0 0 0; 0 -1 0 0 0; 0 0 -1 0 0; 0 0 0 -1 0],
+    [0 0 0 0 -1; 1 0 0 0 0; 0 1 0 0 0; 0 0 1 0 0; 0 0 0 -1 0],
+    [0 0 0 0 -1; 1 0 0 0 0; 0 -1 0 0 0; 0 0 1 0 0; 0 0 0 1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 0 0 0; 0 0 -1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 -1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 -1 0 0 0 0; 0 0 1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 -1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 1 0 0; 0 0 -1 0 0 0; 0 0 0 1 0 0; 0 0 0 0 -1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 1 0 0 1 0; 0 0 -1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 -1 0 0 -1 0; 0 0 1 0 0 0; 0 0 0 -1 0 0; 0 0 0 0 1 0],
+    [0 0 0 0 0 -1; 1 0 0 0 0 0; 0 -1 0 0 0 0; 0 0 1 0 0 0; 0 0 0 1 0 0; 0 0 0 0 1 0],
+]
+
+for network in nf_networks
+    @test is_negative_feedback_network(network) == true
+end
+
+for network in non_nf_networks
+    @test is_negative_feedback_network(network) == false
+end
+
+# Test node_coherence
+node_inputs = [0 0 0 0 0 0]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "unknown"
+
+node_inputs = [0 0 1 -1 0 0]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "incoherent"
+
+node_inputs = [0 0 1 -1 0 1]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "incoherent"
+
+node_inputs = [1 0 1 -1 0 1]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "incoherent"
+
+node_inputs = [1 0 1 1 0 1]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "coherent"
+
+node_inputs = [1 -1 1 1 -1 1]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "incoherent"
+
+node_inputs = [0 0 1 0 0 0]
+node_coherence = calculate_node_coherence(node_inputs)
+@test node_coherence == "unknown"
+
 # Test is_directed_cycle_graph function
 @test is_directed_cycle_graph([0 1 0; 0 0 1; 1 0 0])  # forward cycle
 @test is_directed_cycle_graph([0 0 1; 1 0 0; 0 1 0])  # backward cycle
@@ -168,4 +274,4 @@ p2 = [0 0 0 0 -1; -1 0 0 0 0; 0 -1 0 0 0; 0 0 1 0 0; 0 0 0 1 0]
 @test is_same_set_of_networks(unique_network_additions(t2, 1), unique_cycle_addition(t2))
 @test is_same_set_of_networks(unique_network_additions(s1, 1), unique_cycle_addition(s1))
 @test is_same_set_of_networks(unique_network_additions(s3, 1), unique_cycle_addition(s3))
-@test is_same_set_of_networks(unique_network_additions(p2, 1), unique_cycle_addition(p2))
+@test is_same_set_of_networks(unique_network_additions(p2, 1), unique_cycle_addition(p2))

test/runtests.jl

@@ -2,6 +2,7 @@ using Test
 
 @testset "Protein Interaction Networks" begin include("protein_interaction_network/pin_tests.jl") end
 @testset "Gene Regulatory Networks" begin include("gene_regulatory_network/grn_tests.jl") end
+@testset "User Input Handling" begin include("user_input_handling_tests.jl") end
 @testset "Feature Calculation" begin include("feature_calculation_tests.jl") end
 @testset "Network Utilities" begin include("network_utilities_tests.jl") end
 @testset "Model Simulation" begin include("simulation_tests.jl") end

test/user_input_handling_tests.jl

@@ -0,0 +1,18 @@
+using BiologicalOscillations
+
+# Test is_valid_connectivity
+valid_connectivity = [0 0 1; 1 0 0; 0 -1 0]
+result, errmsg = is_valid_connectivity(valid_connectivity)
+@test result == true
+@test errmsg == ""
+
+invalid_connectivity = [0 0 1; 1 0 0; 0 -1 2]
+result, errmsg = is_valid_connectivity(invalid_connectivity)
+@test result == false
+@test errmsg == "Only -1, 0, and 1 are allowed as connectivity values"
+
+# Test connectivity_string_to_matrix
+connectivity_string = "[0 0 1; 1 0 0; 0 -1 0]"
+valid_connectivity = [0 0 1; 1 0 0; 0 -1 0]
+connectivity_matrix = connectivity_string_to_matrix(connectivity_string)
+@test connectivity_matrix == valid_connectivity