specter changes

rules/clustering.smk

@@ -35,8 +35,8 @@ rule specter:
                downsampling = "0" if config["downsampling"]["downsampling_method"] =="normal" else "1"
         shell:
                """
-               cd scripts/Specter/
-               matlab -r 'n_clusters={params.number_of_clusters};ensemble_size={params.ensemble_size};mingamma={params.mingamma};downsampling=string({params.downsampling});' < Specter_demo.m 
+               cd scripts/
+               matlab -r 'n_clusters={params.number_of_clusters};ensemble_size={params.ensemble_size};mingamma={params.mingamma};downsampling=string({params.downsampling});' < Specter.m 
                """
 	
 rule clustering_specter:

scripts/Specter.m

+% load all necessary library
+addpath('Specter/dimred');
+addpath('Specter/LSC');
+addpath('Specter/utils');
+addpath('Specter');
+format short g;
+
+%% read gene expression data: rows are cells, collumns are features (PCs, genes)
+if downsampling == "0"
+  data = csvread("../file_dir/specter_pca_data_normal.csv");
+else
+  data = csvread("../file_dir/specter_pca_data_sphetcher.csv");
+end
+
+specter_labels = eval_auto_Specter(data, n_clusters, ensemble_size, mingamma);
+
+csvwrite("../file_dir/specter_clustering.csv", specter_labels);