Added clustering as in the scverse + edited bugs in readme

README.md

@@ -44,10 +44,10 @@ Starting from an FCS file that is properly transformed, compensated and checked
 import FlowSOM as fs
 
 # Load the FCS file
-ff = fs.main.read_FCS("./tests/data/ff.fcs")
+ff = fs.io.read_FCS("./tests/data/ff.fcs")
 
 # Run the FlowSOM algorithm
-fsom = fs.main.FlowSOM(ff, cols_to_use=[8, 11, 13, 14, 15, 16, 17], xdim=10, ydim=10, n_clus=10)
+fsom = fs.FlowSOM(ff, cols_to_use=[8, 11, 13, 14, 15, 16, 17], xdim=10, ydim=10, n_clus=10)
 
 # Plot the FlowSOM results
 p = fs.pl.plot_stars(fsom, background_values=fsom.get_cluster_data().obs.metaclustering)

src/FlowSOM/__init__.py

@@ -3,7 +3,7 @@
 from . import read_write as io
 from . import preprocessing as pp
 from . import plotting as pl
-from .main import FlowSOM
+from .main import FlowSOM, flowsom_clustering
 
 __all__ = ["plotting", "main"]
 

src/FlowSOM/main.py

@@ -21,7 +21,7 @@ class FlowSOM:
 
     """
 
-    def __init__(self, inp, cols_to_use: np.array = None, n_clus=10, max_meta=None, seed: int = None, **kwargs):
+    def __init__(self, inp, cols_to_use: np.array = None, n_clus=10, seed: int = None, **kwargs):
         """Initialize the FlowSOM AnnData object
 
         :param inp: A file path to an FCS file or a AnnData FCS file to cluster
@@ -30,8 +30,6 @@ def __init__(self, inp, cols_to_use: np.array = None, n_clus=10, max_meta=None,
         :type cols_to_use: np.array
         :param n_clus: The number of metacluster
         :type n_clus: int
-        :param max_meta: To be adapted
-        :type max_meta: int
         :param seed: A fixed seed
         :type seed: int
         """
@@ -423,3 +421,17 @@ def get_cell_data(self):
 
     def get_cluster_data(self):
         return self.mudata["cluster_data"]
+
+
+def flowsom_clustering(inp, cols_to_use=None, n_clus=10, xdim=10, ydim=10, seed=None, **kwargs):
+    """Perform FlowSOM clustering on an anndata object and returns the anndata
+       object with the FlowSOM clusters and metaclusters added as variable
+
+    :param inp: An anndata or filepath to an FCS file
+    :type inp: ad.AnnData / str
+    """
+    fsom = FlowSOM(inp, cols_to_use=cols_to_use, n_clus=n_clus, xdim=xdim, ydim=ydim, seed=seed, **kwargs)
+    inp.obs["FlowSOM_clusters"] = fsom.mudata["cell_data"].obs["clustering"]
+    inp.obs["FlowSOM_metaclusters"] = fsom.mudata["cell_data"].obs["metaclustering"]
+    inp.uns["FlowSOM"] = {"cols_to_use": cols_to_use, "n_clus": n_clus, "xdim": xdim, "ydim": ydim, "seed": seed}
+    return inp

tests/test_basic.py

@@ -49,6 +49,13 @@ def test_new_data(fcs):
     assert fsom_new.get_cell_data().shape == (999, 18)
 
 
+def test_flowsom_clustering(fcs):
+    inp = fs.flowsom_clustering(fcs, cols_to_use=[8, 11, 13, 14, 15, 16, 17])
+    assert "FlowSOM_clusters" in inp.obs.keys()
+    assert "FlowSOM_metaclusters" in inp.obs.keys()
+    assert "FlowSOM" in inp.uns.keys()
+
+
 def test_aggregate_flowframes():
     new_ff = fs.pp.aggregate_flowframes(
         ["./tests/data/ff.fcs", "./tests/data/ff.fcs"], c_total=5000, channels=[8, 11, 13, 14, 15, 16, 17]