diff --git a/rules/clustering.smk b/rules/clustering.smk index e43d1941014af96f27c7a438245e07214f2c8b89..469c0c8489d7376b50d04e43c19487f4094f6cc3 100644 --- a/rules/clustering.smk +++ b/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: diff --git a/scripts/Specter.m b/scripts/Specter.m new file mode 100644 index 0000000000000000000000000000000000000000..c4016a4034d1952532331bf14b1947c086ea6d4e --- /dev/null +++ b/scripts/Specter.m @@ -0,0 +1,17 @@ +% 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);