Solved incorrect nodes positions and figure size in tree graph

src/lineagetree/_core/utils.py

@@ -79,28 +79,32 @@ def _find_leaves_and_depths_iterative(lnks_tms: dict, root: int) -> tuple[list[i
     leaves : list of int
         List of leaf node ids.
     depths : dict mapping int to int
-        Dictionary mapping node ids to their depth in the tree.
+        Dictionary mapping all node ids to their depth in the tree.
     """
     leaves = []
     depths = {}
+
+    times = lnks_tms["times"]
+    links = lnks_tms["links"]
 
-    # Stack for DFS: (node, current_depth, parent_depth)
+    # Stack for DFS: (node, parent_depth)
     stack = [(root, 0)]
 
     while stack:
-        node, parent_depth = stack.pop()
+        parent_node, parent_depth = stack.pop()
+        depths[parent_node] = parent_depth
+        succ = links.get(parent_node, [])
 
-        node_depth = parent_depth + lnks_tms["times"].get(node, 0)
-        depths[node] = parent_depth
-
-        succ = lnks_tms["links"].get(node, [])
-
         if not succ:  # This is a leaf
-            leaves.append(node)
+            leaves.append(parent_node)
         else:
+            if len(succ) == 1: # in this case, times[parent_node] is equal to the length of the chain
+                child_depth = parent_depth + times[parent_node] - 1
+            else: # in this case, times[parent_node] is 0
+                child_depth = parent_depth + 1
             # Add children to stack (reverse order to maintain left-to-right traversal)
             for child in reversed(succ):
-                stack.append((child, node_depth))
+                stack.append((child, child_depth))
 
     return leaves, depths
 

src/lineagetree/plot.py

@@ -211,7 +211,7 @@ def plot_all_lineages(
     lT: LineageTree,
     nodes: list | None = None,
     last_time_point_to_consider: int | None = None,
-    nrows: int = 2,
+    nrows: int = 1,
     figsize: tuple[int, int] = (10, 15),
     dpi: int = 100,
     fontsize: int = 15,
@@ -232,7 +232,7 @@ def plot_all_lineages(
         For example if start_time is 10, then all trees that begin
         on tp 10 or before are calculated. Defaults to None, where
         it will plot all the roots that exist on `lT.t_b`.
-    nrows : int, default=2
+    nrows : int, default=1
         How many rows of plots should be printed.
     figsize : tuple, default=(10, 15)
         The size of the figure.
@@ -290,7 +290,7 @@ def plot_all_lineages(
             raise Exception(
                 f"Not enough axes, they should be at least {len(graphs)}."
             )
-    flat_axes = axes.flatten()
+    flat_axes = axes.flatten() if hasattr(axes, "flatten") else [axes]
     ax2root = {}
     min_width, min_height = float("inf"), float("inf")
     for ax in flat_axes:
@@ -326,8 +326,8 @@ def plot_all_lineages(
                 "edgecolor": "green",
             },
         )
-    [figure.delaxes(ax) for ax in axes.flatten() if not ax.has_data()]
-    return axes.flatten()[0].get_figure(), axes, ax2root
+    [figure.delaxes(ax) for ax in flat_axes if not ax.has_data()]
+    return flat_axes[0].get_figure(), axes, ax2root
 
 
 def plot_subtree(