pooling experiements set default False & visualization

docs/Config-File.md

@@ -36,8 +36,8 @@ project:
 # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT!
 parameters:
 
-  # If enabled pools multiple experiments from same paper into one experiment; Default: True
-  pool_experiments: True
+  # If enabled pools multiple experiments from same paper into one experiment;
+  pool_experiments: False
 
   # TFCE is a method for multiple comparison correction (Frahm et al., 2022)
   tfce_enabled: True
@@ -46,53 +46,69 @@ parameters:
   gm_masking: True
 
   # Size of bins used in MA histogram
-  bin_steps: 0.0001 # Default: 0.0001
+  # Default: 0.0001
+  bin_steps: 0.0001 
 
   # If enabled uses xgboost models to predict cutoffs instead of monte carlo simulation (Frahm et al., 2024)
   cutoff_predict_enabled: True
 
   # P-value required for significance
   # !! ONLY IF CUTOFF PREDICT IS DISABLED, OTHERWISE WON'T HAVE EFFECT !!
-  significance_threshold: 0.05 # Default: 0.05
+  # Default: 0.05
+  significance_threshold: 0.05
 
   # Preliminary cluster forming threshold used in cluster-level family wise error correction
   # !! ONLY IF CUTOFF PREDICT IS DISABLED, OTHERWISE WON'T HAVE EFFECT !!
-  cluster_forming_threshold: 0.001 # Default: 0.001
+  # Default: 0.001
+  cluster_forming_threshold: 0.001
 
   # Iterations used for monte-carlo based multiple comparison correction 
   # !! ONLY IF CUTOFF PREDICT IS DISABLED, OTHERWISE WON'T HAVE EFFECT !!
-  monte_carlo_iterations: 5000 # Default: 5000
+  # Default: 5000
+  monte_carlo_iterations: 5000
 
   # N subsamples calculated for probabilistic ALE algorithm
-  subsample_n: 2500 # Default: 2500
+  # Default: 2500
+  subsample_n: 2500
 
   # Iterations used in classic contrast algorithm
-  contrast_permutations: 10000 # Default: 10000
+  # Default: 10000
+  contrast_permutations: 10000
 
   # Correction Method on which to base contrast algorithm
-  contrast_correction_method: "cFWE" # Default: "cFWE"; Options: "cFWE", "vFWE", "tfce"
+  # Default: "cFWE"; Options: "cFWE", "vFWE", "tfce"
+  contrast_correction_method: "cFWE"
 
   # Sub-Iterations used in balanced contrast algorithm
-  difference_iterations: 1000 # Default: 1000
+  # Default: 1000
+  difference_iterations: 1000
 
   # Number of parallel processes used for many different steps in the ALE algorith - maximum depends on your machine
-  nprocesses: 2 # Default: 2
-
+  # Default: 2
+  nprocesses: 2 
 
 
 # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT
 
 # MA_Clustering Parameters
 # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT!
 clustering_parameters:
-  max_clusters: 10 # Default: 10
-  subsample_fraction: 0.9 # Default: 0.9
-  sampling_iterations: 1000 # Default: 1000
-  null_iterations: 5000 # Default: 5000
-  correlation_type: "spearman" # Default: "spearman"; Options: "spearman", "pearson"
-  clustering_method: "hierarchical" # Default: "hierarchical"; Options: "hierarchical", "kmeans"
-  linkage_method: "complete" # Default: "complete"; Options: "complete", "average", "ward"
-  use_pooled_std: False # Default: False
+max_clusters: 10                  # Default: 10
+
+subsample_fraction: 0.9           # Default: 0.9
+
+sampling_iterations: 1000          # Default: 1000
+
+null_iterations: 5000             # Default: 5000
+
+correlation_type: "spearman"      # Default: "spearman"; Options: "spearman", "pearson"
+
+clustering_method: "hierarchical" # Default: "hierarchical"; Options: "hierarchical", "kmedoids"
+
+linkage_method: "complete"        # Default: "complete"; Options: "complete", "average"
+
+use_pooled_std: False             # Default: False
+
 # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT
 ```