Merge pull request #28 from pinellolab/add_api

Add API page to readthedocs

docs/source/API.rst

@@ -1,2 +1,74 @@
+.. automodule:: stream2
+
 API
-===
+===
+
+Import stream2 as::
+
+   import stream2 as st2
+
+Configuration for STREAM2
+~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autosummary::
+   :toctree: _autosummary
+
+   settings.set_figure_params
+   settings.set_workdir
+
+
+Reading
+~~~~~~~
+.. autosummary::
+   :toctree: _autosummary
+
+   read_csv
+   read_h5ad
+   read_10X_output
+   read_mtx
+
+
+See more at `anndata <https://anndata.readthedocs.io/en/latest/api.html#reading>`_
+
+
+Preprocessing
+~~~~~~~~~~~~~
+.. autosummary::
+   :toctree: _autosummary
+
+   pp.log_transform
+   pp.normalize
+   pp.cal_qc_rna
+   pp.filter_genes
+   pp.pca
+   pp.select_variable_genes   
+
+
+Tools
+~~~~~
+.. autosummary::
+   :toctree: _autosummary
+
+   tl.dimension_reduction
+   tl.seed_graph
+   tl.learn_graph
+   tl.infer_pseudotime
+   tl.add_path
+   tl.del_path
+   tl.get_weights
+   tl.extend_leaves
+   tl.refit_graph
+   tl.project_graph
+
+
+Plotting
+~~~~~~~~
+.. autosummary::
+   :toctree: _autosummary
+
+   pl.pca_variance_ratio
+   pl.variable_genes
+   pl.violin
+   pl.graph
+   pl.dimension_reduction
+   pl.stream_sc
+   pl.stream

stream2/__init__.py

@@ -7,3 +7,7 @@
 from .readwrite import *
 
 __version__ = "0.1a"
+
+import sys
+sys.modules.update(
+    {f'{__name__}.{m}': globals()[m] for m in ['tl', 'pp', 'pl']})

stream2/_settings.py

@@ -28,10 +28,11 @@ def set_figure_params(
         rc=None,
     ):
         """Set global parameters for figures. Modified from sns.set()
+
         Parameters
         ----------
         context : string or dict
-            Plotting context parameters, see seaborn :func:`plotting_context
+            Plotting context parameters, see seaborn :func:`plotting_context`
         style: `string`,optional (default: 'white')
             Axes style parameters, see seaborn :func:`axes_style`
         palette : string or sequence
@@ -51,6 +52,9 @@ def set_figure_params(
             rc settings properties.
             Parameter mappings to override the values in the preset style.
             Please see https://matplotlib.org/tutorials/introductory/customizing.html#a-sample-matplotlibrc-file # noqa
+
+        Returns
+        -------
         """
         # mpl.rcParams.update(mpl.rcParamsDefault)
         sns.set(

stream2/plotting/_plot.py

@@ -104,7 +104,7 @@ def violin(
             plt.savefig(
                 os.path.join(fig_path, fig_name),
                 pad_inches=1,
-                bbox_inches="tight",dpi=300,
+                bbox_inches="tight", dpi=300,
             )
             plt.close(fig)
     if len(list_var) > 0:
@@ -144,7 +144,7 @@ def violin(
             plt.savefig(
                 os.path.join(fig_path, fig_name),
                 pad_inches=1,
-                bbox_inches="tight",dpi=300,
+                bbox_inches="tight", dpi=300,
             )
             plt.close(fig)
 
@@ -211,7 +211,7 @@ def hist(
             plt.savefig(
                 os.path.join(fig_path, fig_name),
                 pad_inches=1,
-                bbox_inches="tight",dpi=300,
+                bbox_inches="tight", dpi=300,
             )
             plt.close(fig)
     if len(list_var) > 0:
@@ -240,7 +240,7 @@ def hist(
             plt.savefig(
                 os.path.join(fig_path, fig_name),
                 pad_inches=1,
-                bbox_inches="tight",dpi=300,
+                bbox_inches="tight", dpi=300,
             )
             plt.close(fig)
 
@@ -290,7 +290,7 @@ def pca_variance_ratio(
         plt.savefig(
             os.path.join(fig_path, fig_name),
             pad_inches=1,
-            bbox_inches="tight",dpi=300,
+            bbox_inches="tight", dpi=300,
         )
         plt.close(fig)
 
@@ -366,7 +366,7 @@ def pcs_features(
         plt.savefig(
             os.path.join(fig_path, fig_name),
             pad_inches=1,
-            bbox_inches="tight",dpi=300,
+            bbox_inches="tight", dpi=300,
         )
         plt.close(fig)
 
@@ -435,7 +435,7 @@ def variable_genes(
         fig.savefig(
             os.path.join(fig_path, fig_name),
             pad_inches=1,
-            bbox_inches="tight",dpi=300,
+            bbox_inches="tight", dpi=300,
         )
         plt.close(fig)
 
@@ -659,7 +659,7 @@ def _scatterplot2d(
         plt.savefig(
             os.path.join(fig_path, fig_name),
             pad_inches=1,
-            bbox_inches="tight",dpi=300,
+            bbox_inches="tight", dpi=300,
         )
         plt.close(fig)
     if copy:
@@ -1199,7 +1199,7 @@ def graph(
         fig.savefig(
             os.path.join(fig_path, fig_name),
             pad_inches=1,
-            bbox_inches="tight",dpi=300,
+            bbox_inches="tight", dpi=300,
         )
         plt.close(fig)
 
@@ -1592,7 +1592,7 @@ def stream(
     color: `list` optional (default: None)
         Column names of observations (adata.obs.columns)
         or variable names(adata.var_names)
-         A list of names to be plotted.
+        A list of names to be plotted.
     preference: `list`, optional (default: None):
         The preference of nodes. The branch with speficied nodes are preferred
         and will be put on the upper part of stream plot.
@@ -1832,10 +1832,10 @@ def stream(
             if color is None:
                 plt.savefig(os.path.join(
                     file_path_S, 'plot_stream.' + fig_format),
-                    pad_inches=1, bbox_inches='tight',dpi=300)
+                    pad_inches=1, bbox_inches='tight', dpi=300)
             else:
                 plt.savefig(os.path.join(
                     file_path_S,
                     'plot_stream_' + slugify(ann) + '.' + fig_format),
-                    pad_inches=1, bbox_inches='tight',dpi=300)
+                    pad_inches=1, bbox_inches='tight', dpi=300)
             plt.close(fig)

stream2/preprocessing/_general.py

@@ -7,6 +7,7 @@
 
 def log_transform(adata):
     """Return the natural logarithm of one plus the input array, element-wise.
+
     Parameters
     ----------
     adata: AnnData
@@ -25,22 +26,24 @@ def log_transform(adata):
 
 def normalize(adata, method="lib_size", scale_factor=1e4, save_raw=True):
     """Normalize count matrix.
+
     Parameters
     ----------
     adata: AnnData
         Annotated data matrix.
     method: `str`, optional (default: 'lib_size')
-        Choose from {{'lib_size','tf_idf'}}
-        Method used for dimension reduction.
-        'lib_size': Total-count normalize (library-size correct)
+        Choose from {{'lib_size','tf_idf'}}.
+        Method used for dimension reduction.\n
+        'lib_size': Total-count normalize (library-size correct).\n
         'tf_idf': TF-IDF (term frequency–inverse document frequency)
-                  transformation
+                  transformation.
     Returns
     -------
     updates `adata` with the following fields.
     X: `numpy.ndarray` (`adata.X`)
         Store #observations × #var_genes normalized data matrix.
     """
+
     if method not in ["lib_size", "tf_idf"]:
         raise ValueError("unrecognized method '%s'" % method)
     if save_raw:

stream2/preprocessing/_pca.py

@@ -18,6 +18,7 @@ def pca(
     **kwargs,
 ):
     """perform Principal Component Analysis (PCA)
+
     Parameters
     ----------
     adata: AnnData

stream2/preprocessing/_qc.py

@@ -179,6 +179,7 @@ def filter_samples(
     expr_cutoff=1,
 ):
     """Filter out samples based on different metrics.
+
     Parameters
     ----------
     adata: AnnData
@@ -286,6 +287,7 @@ def filter_cells_rna(
     expr_cutoff=1,
 ):
     """Filter out cells for RNA-seq based on different metrics.
+
     Parameters
     ----------
     adata: AnnData
@@ -394,6 +396,7 @@ def filter_cells_atac(
     expr_cutoff=1,
 ):
     """Filter out cells for ATAC-seq based on different metrics.
+
     Parameters
     ----------
     adata: AnnData
@@ -502,6 +505,7 @@ def filter_genes(
     expr_cutoff=1,
 ):
     """Filter out features based on different metrics.
+
     Parameters
     ----------
     adata: AnnData
@@ -616,6 +620,7 @@ def filter_peaks(
     expr_cutoff=1,
 ):
     """Filter out features based on different metrics.
+
     Parameters
     ----------
     adata: AnnData
@@ -730,6 +735,7 @@ def filter_features(
     expr_cutoff=1,
 ):
     """Filter out features based on different metrics.
+
     Parameters
     ----------
     adata: AnnData

stream2/tools/_dimension_reduction.py

@@ -21,7 +21,8 @@ def dimension_reduction(
     eigen_solver="auto",
     **kwargs,
 ):
-    """perform UMAP
+    """perform dimension reduction
+
     Parameters
     ----------
     adata: AnnData