fixed incorrect headers

elkebir-group · Aug 12, 2024 · 7c15716 · 7c15716
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diff --git a/docs/setup/cli.md b/docs/setup/cli.md
@@ -80,12 +80,12 @@ IGHA2
 !!! note "isotype labeling"
     Be sure that the labels used in the encoding file exactly match the labeling syntax in the input data. There is no standard convention for isotype labels,  e.g., IgM, M, IghM and IGHM, and therefore the convention must be provided by the user. 
 
- ### Output
+ #### Output
 
 The main output from the `preprocess` sub-command is the a pickled dictionary storing `Clonotype` objects for each retained clonotype in the data. This output file will be used as the input to the `fit` sub-command. 
 
 
- ### Example
+ #### Example
 
  Here is an example of how to run the preprocess sub-command.
 

diff --git a/docs/setup/package.md b/docs/setup/package.md
@@ -160,7 +160,7 @@ Specifically, in the above examples `best_trees` is a dictionary, with clonotype
 
 A B cell lineage tree for tribal is a rooted tree with nodes labeled by BCR sequences (concentated heavy and optional light chains) and by isotypes. The [LineageTree](../api/lineagetree.md) class also holds the current  SHM parsimony score (`shm_obj`) and CSR likelihood (`csr_obj`). 
 
-A `LineageTree` can be visualized as a `png` or `pdf` via the [draw](../api/lineage_tree.md) function.  Nodes are colored by the isotype via the default `color_encoding`. 
+A `LineageTree` can be visualized as a `png` or `pdf` via the [draw](../api/lineagetree.md) function.  Nodes are colored by the isotype via the default `color_encoding`. 
 
 ```python
  color_encoding =  {
@@ -348,5 +348,6 @@ Lastly, a CSV file with the objective values of each [LineageTree](../api/lineag
 
 ```python
 from tribal import lineage_tree_list
-lineage_tree_list.write("objectives.csv")
+isotypes = ['IGHM', 'IGHG3', 'IGHG1', 'IGHA1','IGHG2','IGHG4','IGHE','IGHA2']
+lineage_tree_list.write("objectives.csv", isotype_encoding=isotypes)
 ```
diff --git a/tribal/lineage_tree.py b/tribal/lineage_tree.py
@@ -419,8 +419,8 @@ def write(self, outpath:str, isotype_encoding=None, tree_label=None):
         ----------
         outpath : str
             the path to file the files should be written.  
-        clonotype : Clonotype, optional
-            the corresponding clonotype object for the lineage tree.  
+        isotype_encoding : list, optional
+            the ordered isotype labels  
         """
         if tree_label is None:
             tree_label = ""
@@ -579,8 +579,8 @@ def write_all(self, outpath, isotype_encoding=None):
         ----------
         outpath : str
             the path to where the files should be written.
-        clonotypes : dict
-            the corresponding Clonotype object for the LineageTreeList
+        isotype_encoding : list
+            the ordered isotype labeles
         """
         for i,lt in enumerate(self):
             lt.write(outpath,isotype_encoding=isotype_encoding, tree_label=i)