all_chain_plotting

src/lineagetree/_mixins/plot_mixin.py

@@ -5,6 +5,7 @@
     plot_dtw_heatmap,
     plot_dtw_trajectory,
     plot_subtree,
+    plot_chain_histogram,
 )
 
 from ._methodize import AutoMethodizeMeta
@@ -19,3 +20,4 @@ class PlotMixin(metaclass=AutoMethodizeMeta):
     plot_dtw_heatmap = plot_dtw_heatmap
     plot_dtw_trajectory = plot_dtw_trajectory
     plot_subtree = plot_subtree
+    plot_chain_histogram = plot_chain_histogram

src/lineagetree/plot.py

@@ -741,3 +741,50 @@ def plot_dtw_trajectory(
         )
 
     return distance, fig
+
+
+def plot_chain_histogram(
+    lT: LineageTree,
+    *,
+    with_leaves: bool = False,
+    with_roots: bool = False,
+    bins: int = None,
+    color: str = "blue",
+    ax: plt.Axes | None = None,
+    **kwargs,
+):
+    """Plot the histograms of the chains length of the dataset. By default the chains tha tcontain root or leaf ndoes are not included.
+
+    Parameters
+    ----------
+    lT : LineageTree
+        The LineageTree instance.
+    with_leaves : bool, optional
+        Include the chains that contain leaves in the histogram, by default False
+    with_roots : bool, optional
+        Include the chains that contain roots in the histogram, by default False
+    bins : int, optional
+        Bins of tghe histogram, if none they are set automatically, by default None
+    color : str, optional
+        Color of the histogram, by default "blue"
+    ax : plt.Axes | None, optional
+        The plt.Axes instance, if None it creates a new Axes instance, by default None
+
+    Returns
+    -------
+    plt.Figure
+        The matplotlib figure
+    plt.Axes
+        The matplotlib axes
+    """
+
+    list_of_chains = [c for c in lT.all_chains]
+    if not with_roots:
+        list_of_chains = [c for c in list_of_chains if c[0] not in lT.roots]
+    if not with_leaves:
+        list_of_chains = [c for c in list_of_chains if c[-1] not in lT.leaves]
+    chain_lens = [len(c) for c in list_of_chains]
+    if not ax:
+        _, ax = plt.subplots(nrows=1, ncols=1, **kwargs)
+    ax.hist(chain_lens, bins, color=color)
+    return ax.get_figure(), ax

tests/test_lineageTree.py

@@ -750,3 +750,24 @@ def test_change_labels():
         24: "left",
         25: "left",
     }
+
+
+def test_plot_chain_hist():
+    _, ax1 = lt.plot_chain_histogram()
+    _, ax2 = lt.plot_chain_histogram(with_leaves=True)
+    _, ax3 = lt.plot_chain_histogram(with_roots=True)
+    _, ax4 = lt.plot_chain_histogram(with_roots=True, with_leaves=True)
+    assert sum(p.get_height() for p in ax4.patches) == len(lt.all_chains)
+    assert sum(p.get_height() for p in ax3.patches) == (
+        len(lt.all_chains) - len(lt.leaves)
+    )
+    assert sum(p.get_height() for p in ax2.patches) == (
+        len(lt.all_chains) - len(lt.roots)
+    )
+    print(
+        sum(p.get_height() for p in ax1.patches),
+        len(lt.all_chains) - len(lt.leaves) - len(lt.roots),
+    )
+    assert sum(p.get_height() for p in ax1.patches) == (
+        len(lt.all_chains) - len(lt.leaves.union(lt.roots))
+    )