Merge pull request #152 from BiomedicalMachineLearning/prepare

update: config and docs for 0.4.0
BiomedicalMachineLearning · Feb 3, 2022 · 5ebea70 · 5ebea70
2 parents 45a1574 + 782b719
commit 5ebea70
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,6 +11,6 @@ repos:
     -   id: requirements-txt-fixer
 
 -   repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 22.1.0
     hooks:
     -   id: black
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,8 @@
 History
 =======
 
+0.4.0 (2022-02-03)
+------------------
 0.3.2 (2021-03-29)
 ------------------
 0.3.1 (2020-12-24)

diff --git a/docs/api.rst b/docs/api.rst
@@ -107,6 +107,7 @@ Spatial: `spatial`
    spatial.trajectory.compare_transitions
    spatial.trajectory.detect_transition_markers_clades
    spatial.trajectory.detect_transition_markers_branches
+   spatial.trajectory.set_root
 
 .. module:: stlearn.spatial.morphology
 .. currentmodule:: stlearn
@@ -145,13 +146,12 @@ Tools: `tl`
 .. autosummary::
    :toctree: .
 
-   tl.cci.lr
-   tl.cci.het.count
-   tl.cci.het.create_grids
-   tl.cci.het.count_grid
-   tl.cci.merge
-   tl.cci.permutation
-
+   tl.cci.load_lrs
+   tl.cci.grid
+   tl.cci.run
+   tl.cci.adj_pvals
+   tl.cci.run_lr_go
+   tl.cci.run_cci
 
 Plot: `pl`
 -------------------
@@ -162,6 +162,7 @@ Plot: `pl`
 .. autosummary::
    :toctree: .
 
+   pl.QC_plot
    pl.gene_plot
    pl.gene_plot_interactive
    pl.cluster_plot
@@ -170,11 +171,20 @@ Plot: `pl`
    pl.subcluster_plot
    pl.non_spatial_plot
    pl.deconvolution_plot
-   pl.QC_plot
-   pl.het_plot
-   pl.het_plot_interactive
-   pl.grid_plot
    pl.plot_mask
+   pl.lr_summary
+   pl.lr_diagnostics
+   pl.lr_n_spots
+   pl.lr_go
+   pl.lr_result_plot
+   pl.lr_plot
+   pl.cci_check
+   pl.ccinet_plot
+   pl.lr_chord_plot
+   pl.lr_cci_map
+   pl.cci_map
+   pl.lr_plot_interactive
+   pl.spatialcci_plot_interactive
 
 .. module:: stlearn.pl.trajectory
 .. currentmodule:: stlearn

diff --git a/docs/conf.py b/docs/conf.py
@@ -27,7 +27,7 @@
 import os
 
 if not os.path.isdir("./_static"):
-    url = "https://www.dropbox.com/s/mky2cp1ksjc4bes/downloads.zip"
+    url = "https://www.dropbox.com/s/6mgg4p978zwyxy9/download.zip?dl=1"
     os.system("wget " + url)
     os.system("unzip downloads.zip")
 
@@ -75,7 +75,7 @@
 
 # General information about the project.
 project = "stLearn"
-copyright = "2020, Genomics and Machine Learning lab"
+copyright = "2022, Genomics and Machine Learning lab"
 author = "Genomics and Machine Learning lab"
 
 # The version info for the project you're documenting, acts as replacement
@@ -199,7 +199,7 @@ def setup(app):
     "tutorials/stSME_clustering": "_static/img/thumbnail/sme.png",
     "tutorials/stSME_comparison": "_static/img/thumbnail/com.png",
     "tutorials/Pseudo-time-space-tutorial": "_static/img/thumbnail/psts.png",
-    "tutorials/stLearn-CCI": "_static/img/thumbnail/cci_rank.png",
+    "tutorials/stLearn-CCI": "_static/img/thumbnail/cci.png",
     "tutorials/Read_MERFISH": "_static/img/thumbnail/mer.png",
     "tutorials/Read_seqfish": "_static/img/thumbnail/seq.png",
     "tutorials/Working-with-Old-Spatial-Transcriptomics-data": "_static/img/thumbnail/legacy.png",
@@ -209,23 +209,5 @@ def setup(app):
     "tutorials/Working_with_scanpy": "_static/img/thumbnail/scanpy.png",
     "tutorials/Core_plots": "_static/img/thumbnail/core_plots.png",
     "tutorials/Read_any_data": "_static/img/thumbnail/any.png",
+    "tutorials/Integration_multiple_datasets": "_static/img/thumbnail/integrate.png",
 }
-
-
-# import nbclean, glob
-# from pathlib import Path
-
-# for filename in glob.glob('../tutorials/*.ipynb', recursive=True):
-#    Path(filename).rename(filename.split("/")[-1])
-
-
-# with open("./list_tutorial.txt") as f:
-#     content = f.readlines()
-
-# content = [x.strip() for x in content]
-
-
-# for filename in glob.glob('*.ipynb', recursive=True):
-#     ntbk = nbclean.NotebookCleaner(filename)
-#     ntbk.clear('stderr')
-#     ntbk.save(filename)
diff --git a/docs/index.rst b/docs/index.rst
@@ -37,9 +37,13 @@ In the new release, we provide the interactive plots:
 Latest additions
 ----------------
 
+.. include:: release_notes/0.4.0.rst
+
 .. include:: release_notes/0.3.2.rst
 
 
+
+
 .. toctree::
    :maxdepth: 1
    :hidden:

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -57,13 +57,11 @@ Access to:
 
  - https://www.lfd.uci.edu/~gohlke/pythonlibs/#louvain-igraph
 
-Download 2 files: python_igraph‑0.7.1.post6‑cp38‑cp38‑win_amd64.whl and louvain‑0.6.1‑cp38‑cp38‑win_amd64.whl
+ - https://www.lfd.uci.edu/~gohlke/pythonlibs/#leidenalg
 
-You have to change to downloaded files directory and install it:
-::
+Download 3 files: igraph‑0.9.9‑cp38‑cp38‑win_amd64.whl, louvain‑0.7.1‑cp38‑cp38‑win_amd64.whl, leidenalg‑0.8.8‑cp38‑cp38‑win_amd64.whl
 
-	pip install python_igraph‑0.7.1.post6‑cp38‑cp38‑win_amd64.whl
-	pip install louvain‑0.6.1‑cp38‑cp38‑win_amd64.whl
+You have to change to downloaded files directory and install those packages.
 
 **Step 4:**
 

diff --git a/docs/release_notes/0.4.0.rst b/docs/release_notes/0.4.0.rst
@@ -0,0 +1,8 @@
+0.4.0 `2022-02-03`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Feature
+
+- Upgrade stSME, PSTS and CCI analysis methods.
+
+- Add CCI analysis functions: :func:`~stlearn.tl.cci.load_lrs`, :func:`~stlearn.tl.cci.grid`, :func:`~stlearn.tl.cci.run`, :func:`~stlearn.tl.cci.adj_pvals`, :func:`~stlearn.tl.cci.run_lr_go`, :func:`~stlearn.pl.lr_summary`, :func:`~stlearn.pl.lr_diagnostics`, :func:`~stlearn.pl.lr_n_spots`, :func:`~stlearn.pl.lr_go`, :func:`~stlearn.pl.lr_result_plot`, :func:`~stlearn.pl.lr_plot`, :func:`~stlearn.pl.cci_check`, :func:`~stlearn.pl.ccinet_plot`, :func:`~stlearn.pl.lr_chord_plot`, :func:`~stlearn.pl.lr_cci_map`, :func:`~stlearn.pl.cci_map`, :func:`~stlearn.pl.lr_plot_interactive`, :func:`~stlearn.pl.spatialcci_plot_interactive`
diff --git a/docs/release_notes/index.rst b/docs/release_notes/index.rst
@@ -5,3 +5,5 @@ Version 0.3.2
 ---------------------------
 
 .. include:: 0.3.2.rst
+
+.. include:: 0.4.0.rst
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,14 +1,15 @@
 -r ../requirements.txt
 ipyvolume==0.6.0a1
 ipywebrtc
-ipywidgets>=7.4.0
+ipywidgets
 jupyter_sphinx==0.1.4
 nbclean>=0.3.2
-nbformat==4.4.0
+nbformat
 nbsphinx>=0.7.0
 pygments >= 2.4.1
+recommonmark
 sphinx==3.0.0
 sphinx-autodoc-typehints
 sphinx_gallery
 sphinx_rtd_theme>=0.3.1
-typing_extensions; python_version < '3.8'
+typing_extensions
diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,7 @@
 bokeh == 2.3.0
+numba==0.53.1
 #fa2 == 0.3.5
 Pillow==9.0.0
 scanpy==1.8.2
 scikit-image==0.18.2
 tensorflow==2.7.0
-numba==0.53.1
diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.2
+current_version = 0.4.0
 commit = True
 tag = True
 

diff --git a/setup.py b/setup.py
@@ -21,16 +21,13 @@
 setup(
     author="Genomics and Machine Learning lab",
     author_email="duy.pham@uq.edu.au",
-    python_requires=">=3.5",
+    python_requires=">=3.8",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Developers",
         "License :: OSI Approved :: BSD License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
     description="A downstream analysis toolkit for Spatial Transcriptomic data",
@@ -50,6 +47,6 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/BiomedicalMachineLearning/stLearn",
-    version="0.3.2",
+    version="0.4.0",
     zip_safe=False,
 )
diff --git a/stlearn/__init__.py b/stlearn/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Genomics and Machine Learning lab"""
 __email__ = "duy.pham@uq.edu.au"
-__version__ = "0.3.1"
+__version__ = "0.4.0"
 
 
 from . import add

diff --git a/stlearn/plotting/cci_plot.py b/stlearn/plotting/cci_plot.py
@@ -45,7 +45,7 @@
 from bokeh.io import push_notebook, output_notebook
 from bokeh.plotting import show
 
-# Functions for visualising the overall LR results and diagnostics.
+#### Functions for visualising the overall LR results and diagnostics.
 
 
 def lr_diagnostics(
@@ -325,6 +325,7 @@ def lr_go(
         show_all=n_top <= max_text,
     )
 
+
 def cci_check(
     adata: AnnData,
     use_label: str,
@@ -537,6 +538,7 @@ def lr_result_plot(
         vmax,
     )
 
+
 # TODO finish writing the documentation for this parameter.
 # @_docs_params(het_plot=doc_lr_plot)
 def lr_plot(
@@ -566,7 +568,7 @@ def lr_plot(
     sig_cci: bool = False,
     lr_colors: dict = None,
     figsize: tuple = (6.4, 4.8),
-    use_mix: None,
+    use_mix=None,
     # plotting params
     **kwargs,
 ) -> Optional[AnnData]:
@@ -959,6 +961,7 @@ def het_plot(
 # Functions relating to visualising celltype-celltype interactions after
 # calling: st.tl.cci_rank.run_cci
 
+
 def ccinet_plot(
     adata: AnnData,
     use_label: str,
@@ -1360,6 +1363,7 @@ def lr_chord_plot(
     else:
         return fig, ax
 
+
 def grid_plot(
     adata,
     use_label: str = None,

diff --git a/stlearn/plotting/classes_bokeh.py b/stlearn/plotting/classes_bokeh.py
@@ -1161,7 +1161,7 @@ def update_data(self, attrname, old, new):
         self.layout.children[1] = self.make_fig()
 
     def _get_cci_lr_edges(self):
-        """ Gets edge list of significant interactions for LR pair. """
+        """Gets edge list of significant interactions for LR pair."""
 
         adata = self.adata[0]
         lr = self.lr_select.value

diff --git a/stlearn/spatials/SME/_weighting_matrix.py b/stlearn/spatials/SME/_weighting_matrix.py
@@ -55,7 +55,7 @@ def calculate_weight_matrix(
             adata.obs[["imagecol", "imagerow"]],
             metric="euclidean",
         )
-        unit = math.sqrt(reg_row.coef_ ** 2 + reg_col.coef_ ** 2)
+        unit = math.sqrt(reg_row.coef_**2 + reg_col.coef_**2)
         pd_norm = np.where(pd >= unit, 0, 1)
 
         md = 1 - pairwise_distances(
@@ -75,7 +75,7 @@ def calculate_weight_matrix(
 
     else:
         pd = pairwise_distances(adata.obs[["imagecol", "imagerow"]], metric="euclidean")
-        unit = math.sqrt(reg_row.coef_ ** 2 + reg_col.coef_ ** 2)
+        unit = math.sqrt(reg_row.coef_**2 + reg_col.coef_**2)
         pd_norm = np.where(pd >= rate * unit, 0, 1)
 
         md = 1 - pairwise_distances(adata.obsm["X_morphology"], metric="cosine")

diff --git a/stlearn/spatials/SME/impute.py b/stlearn/spatials/SME/impute.py
@@ -257,7 +257,7 @@ def pseudo_spot(
 
     point_tree = scipy.spatial.cKDTree(coor)
     n_neighbour = []
-    unit = math.sqrt(reg_row.coef_ ** 2 + reg_col.coef_ ** 2)
+    unit = math.sqrt(reg_row.coef_**2 + reg_col.coef_**2)
     for i in range(len(impute_coor)):
         current_neighbour = point_tree.query_ball_point(
             impute_coor.values[i], round(unit)

diff --git a/stlearn/spatials/trajectory/utils.py b/stlearn/spatials/trajectory/utils.py
@@ -582,7 +582,7 @@ def _mat_mat_corr_sparse(
 
     X_bar = np.reshape(np.array(X.mean(axis=1)), (-1, 1))
     X_std = np.reshape(
-        np.sqrt(np.array(X.power(2).mean(axis=1)) - (X_bar ** 2)), (-1, 1)
+        np.sqrt(np.array(X.power(2).mean(axis=1)) - (X_bar**2)), (-1, 1)
     )
 
     y_bar = np.reshape(np.mean(Y, axis=0), (1, -1))

diff --git a/stlearn/tools/microenv/cci/analysis.py b/stlearn/tools/microenv/cci/analysis.py
@@ -296,7 +296,9 @@ def run(
         count(adata, distance=distance, use_label=use_label, use_het=use_label)
 
     het_vals = (
-        np.array([1] * len(adata)) if use_label not in adata.obsm else adata.obsm[use_label]
+        np.array([1] * len(adata))
+        if use_label not in adata.obsm
+        else adata.obsm[use_label]
     )
 
     """ 1. Filter any LRs without stored expression.

diff --git a/stlearn/tools/microenv/cci/het_helpers.py b/stlearn/tools/microenv/cci/het_helpers.py
@@ -223,7 +223,7 @@ def get_data_for_counting(adata, use_label, mix_mode, all_set):
 
 
 def get_neighbourhoods(adata):
-    """ Gets the neighbourhood information. """
+    """Gets the neighbourhood information."""
 
     # Old stlearn version where didn't store neighbourhood barcodes, not good
     #   for anndata subsetting!!

diff --git a/stlearn/tools/microenv/cci/perm_utils.py b/stlearn/tools/microenv/cci/perm_utils.py
@@ -10,7 +10,7 @@
 
 
 def nonzero_quantile(expr, q, interpolation):
-    """ Calculating the non-zero quantiles. """
+    """Calculating the non-zero quantiles."""
     nonzero_expr = expr[expr > 0]
     quants = np.quantile(nonzero_expr, q=q, interpolation=interpolation)
     if type(quants) != np.array and type(quants) != np.ndarray:
@@ -19,7 +19,7 @@ def nonzero_quantile(expr, q, interpolation):
 
 
 def getzero_prop(expr):
-    """ Calculating the proportion of zeros. """
+    """Calculating the proportion of zeros."""
     zero_bool = expr == 0
     n_zeros = len(np.where(zero_bool)[0])
     zero_prop = [n_zeros / len(expr)]

diff --git a/stlearn/tools/microenv/cci/permutation.py b/stlearn/tools/microenv/cci/permutation.py
@@ -497,7 +497,7 @@ def get_stats(
         mu = np.exp(res.params[0])
         alpha = res.params[1]
         Q = 0
-        size = 1.0 / alpha * mu ** Q
+        size = 1.0 / alpha * mu**Q
         prob = size / (size + mu)
 
         if return_negbinom_params:  # For testing purposes #