Merge branch 'main' of https://github.com/halbritter-lab/kidney-genetics

halbritter-lab · May 14, 2024 · dc871f7 · dc871f7
2 parents 1ac546c + 52a16c8
commit dc871f7
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/analyses/D_ProteinInteractionAnalysis/D_ProteinInteractionAnalysis.R b/analyses/D_ProteinInteractionAnalysis/D_ProteinInteractionAnalysis.R
@@ -169,6 +169,7 @@ max_groups_full <- read.csv("results/disease_group_STRING_cluster_indices_min_ge
 
 # example plot of kidney disease group distribution within subcluster
 ex1 <- plot_disease_group_distribution(subcluster="3-1", max_groups_full)
+ex1
 ############################################
 
 
@@ -198,11 +199,11 @@ ial_plot3 <- plot_network_by_level(index_genes = c("9606.ENSP00000363973", "9606
                                    max_level = 1)
 
 # TODO: correct Error if edgelist is empty, e.g.:
-# ia_plot2 <- plot_network_of_index_gene(index_gene = "9606.ENSP00000239891",
-#                                        string_db = string_db_full,
-#                                        min_comb_score = 890,
-#                                        STRING_id_vec = STRING_id_vec,
-#                                        disease_group_df = max_groups_full)
+ia_plot_error <- plot_network_of_index_gene(index_gene = "9606.ENSP00000239891",
+                                       string_db = string_db_full,
+                                       min_comb_score = 810, #810 works, 820 error,  890 different error
+                                       STRING_id_vec = STRING_id_vec,
+                                       disease_group_df = max_groups_full)
 
 
 ############################################

diff --git a/analyses/functions/protein_interaction_analysis-functions.R b/analyses/functions/protein_interaction_analysis-functions.R
@@ -232,7 +232,6 @@ create_edgelist <- function(connection_df, all_contacts, min_comb_score, symbol_
 
 # function to plot the interaction network given by an edgelist. The index gene symbols have a square marker
 plot_interaction_network <- function(edgelist, disease_group_df, index_gene_symbols){
-  print(edgelist)
   # create a network from the edgelist
   netw <- network(edgelist, directed = F)
 
@@ -348,7 +347,8 @@ plot_network_of_index_gene <- function(index_gene, string_db, min_comb_score, ST
 
   # plot interaction network of index gene
   interaction_plot <- plot_interaction_network(edgelist = edgelist,
-                                               disease_group_df = disease_group_df)
+                                               disease_group_df = disease_group_df,
+                                               index_gene_symbols = c(index_gene))
 
   return(interaction_plot)
 }