diff --git a/docs/tutorials/quickstart.ipynb b/docs/tutorials/quickstart.ipynb index 4067e8c..5bd91ac 100644 --- a/docs/tutorials/quickstart.ipynb +++ b/docs/tutorials/quickstart.ipynb @@ -65,7 +65,17 @@ "metadata": {}, "outputs": [], "source": [ - "pm.pp.split_signal(adata)" + "pm.pp.split_signal(adata, var_key=\"channel\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2b1204cf", + "metadata": {}, + "outputs": [], + "source": [ + "pm.pl.plotdata(adata)" ] }, { diff --git a/pytometry/__init__.py b/pytometry/__init__.py index 6222248..8dfc6f0 100644 --- a/pytometry/__init__.py +++ b/pytometry/__init__.py @@ -26,5 +26,3 @@ from . import preprocessing as pp from . import read_write as io from . import tools as tl - -# from ._core import ExampleClass, example_function # noqa diff --git a/pytometry/_core.py b/pytometry/_core.py deleted file mode 100644 index f6882ed..0000000 --- a/pytometry/_core.py +++ /dev/null @@ -1,26 +0,0 @@ -def example_function(column_name: str) -> str: - """Lower case your input string. - - Args: - column_name: Column name to transform to lower case. - - Returns: - The lower-cased column name. - """ - return column_name.lower() - - -class ExampleClass: - """Awesome class.""" - - def __init__(self, value: int): - print("initializing") - - def bar(self) -> str: - """Bar function.""" - return "hello" - - @property - def foo(self) -> str: - """Foo property.""" - return "hello" diff --git a/pytometry/plotting/_histogram.py b/pytometry/plotting/_histogram.py index 483d5bf..700eccc 100644 --- a/pytometry/plotting/_histogram.py +++ b/pytometry/plotting/_histogram.py @@ -49,7 +49,7 @@ def plotdata( " normalization." ) - if option_key not in ["area", "height", "other"]: + if option_key.lower() not in ["area", "height", "other"]: print(f"Option {option_key} is not a valid category. Return all.") datax = adata_.X var_names = adata_.var_names.values @@ -71,10 +71,10 @@ def plotdata( number = len(names) columns = 3 - rows = np.ceil(number / columns) + rows = int(np.ceil(number / columns)) fig = plt.figure() - fig.subplots_adjust(hspace=0.4, wspace=0.6) + fig.subplots_adjust(hspace=0.8, wspace=0.6) for idx in range(number): ax = fig.add_subplot(rows, columns, idx + 1)