gsMap 1.60__py3-none-any.whl

gsMap/visualize.py

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+import argparse
+from pathlib import Path
+from typing import Literal
+
+import scanpy as sc
+import numpy as np
+import pandas as pd
+import plotly.express as px
+from gsMap.config import VisualizeConfig, add_Visualization_args
+
+
+def load_ldsc(ldsc_input_file):
+    ldsc = pd.read_csv(ldsc_input_file, compression='gzip')
+    ldsc.spot = ldsc.spot.astype(str).replace('\.0', '', regex=True)
+    ldsc.index = ldsc.spot
+    ldsc['logp'] = -np.log10(ldsc.p)
+    return ldsc
+
+
+# %%
+def load_st_coord(adata, ldsc, annotation):
+    spot_name = adata.obs_names.to_list()
+    space_coord = pd.DataFrame(adata.obsm['spatial'], columns=['sx', 'sy'], index=spot_name)
+    space_coord = space_coord[space_coord.index.isin(ldsc.spot)]
+    space_coord_concat = pd.concat([space_coord.loc[ldsc.spot], ldsc.logp], axis=1)
+    space_coord_concat.head()
+    if annotation is not None:
+        annotation = pd.Series(adata.obs[annotation].values, index=adata.obs_names, name='annotation')
+        space_coord_concat = pd.concat([space_coord_concat, annotation], axis=1)
+    return space_coord_concat
+
+
+# %%
+def draw_scatter(space_coord_concat, title=None, fig_style: Literal['dark', 'light'] = 'light',
+                 point_size: int = None, width=800, height=600, annotation=None):
+    # change theme to plotly_white
+    if fig_style == 'dark':
+        px.defaults.template = "plotly_dark"
+    else:
+        px.defaults.template = "plotly_white"
+
+    custom_color_scale = [
+        (1, '#d73027'),  # Red
+        (7 / 8, '#f46d43'),  # Red-Orange
+        (6 / 8, '#fdae61'),  # Orange
+        (5 / 8, '#fee090'),  # Light Orange
+        (4 / 8, '#e0f3f8'),  # Light Blue
+        (3 / 8, '#abd9e9'),  # Sky Blue
+        (2 / 8, '#74add1'),  # Medium Blue
+        (1 / 8, '#4575b4'),  # Dark Blue
+        (0, '#313695')  # Deep Blue
+    ]
+    # custom_color_scale = px.colors.diverging.balance
+    custom_color_scale.reverse()
+    fig = px.scatter(
+        space_coord_concat,
+        x='sx',
+        y='sy',
+        color='logp',  # Color the points by the 'logp' column
+        symbol='annotation' if annotation is not None else None,
+        title=title,
+        color_continuous_scale=custom_color_scale,
+        range_color=[0, max(space_coord_concat.logp)],
+    )
+
+    if point_size is not None:
+        fig.update_traces(marker=dict(size=point_size))
+
+    fig.update_layout(legend_title_text='Annotation')
+
+    fig.update_layout(
+        autosize=False,
+        width=width,
+        height=height,
+    )
+
+    # Adjusting the legend
+    fig.update_layout(
+        legend=dict(
+            yanchor="top",
+            y=0.99,
+            xanchor="left",
+            x=-0.39,
+            font=dict(
+                size=10,
+            )
+        )
+    )
+    # change color bar title
+    fig.update_layout(coloraxis_colorbar_title='-log10(p)')
+
+    return fig
+
+
+def run_Visualize(config: VisualizeConfig):
+    print(f'------Loading LDSC results of {config.input_ldsc_dir}...')
+    ldsc = load_ldsc(ldsc_input_file=Path(config.input_ldsc_dir) / f'{config.sample_name}_{config.trait_name}.csv.gz')
+
+    print(f'------Loading ST data of {config.sample_name}...')
+    adata = sc.read_h5ad(f'{config.input_hdf5_path}')
+
+    space_coord_concat = load_st_coord(adata, ldsc, annotation=config.annotation)
+    fig = draw_scatter(space_coord_concat,
+                       title=config.fig_title,
+                       fig_style=config.fig_style,
+                       point_size=config.point_size,
+                       width=config.fig_width,
+                       height=config.fig_height,
+                       annotation=config.annotation
+                       )
+
+    # save the figure to html
+
+    # Visualization
+    output_dir = Path(config.output_figure_dir)
+    output_dir.mkdir(parents=True, exist_ok=True, mode=0o755)
+    output_file_html = output_dir / f'{config.sample_name}_{config.trait_name}.html'
+    output_file_pdf = output_dir / f'{config.sample_name}_{config.trait_name}.pdf'
+
+    fig.write_html(str(output_file_html))
+    fig.write_image(str(output_file_pdf))
+
+    print(
+        f'------The visualization result is saved in a html file: {output_file_html} which can interactively viewed in a web browser and a pdf file: {output_file_pdf}.')
+
+
+if __name__ == '__main__':
+    TEST = True
+    if TEST:
+        test_dir = '/storage/yangjianLab/chenwenhao/projects/202312_gsMap/data/gsMap_test/Nature_Neuroscience_2021'
+        name = 'E16.5_E1S1'
+
+        config = VisualizeConfig(
+            input_hdf5_path=f'/storage/yangjianLab/songliyang/SpatialData/Data/Embryo/Mice/Cell_MOSTA/h5ad/E16.5_E1S1.MOSTA.h5ad',
+            input_ldsc_dir=
+            f'/storage/yangjianLab/songliyang/SpatialData/Data/Embryo/Mice/Cell_MOSTA/ldsc_enrichment_frac/E16.5_E1S1/',
+            output_figure_dir='/storage/yangjianLab/chenwenhao/projects/202312_gsMap/data/gsMap_test/Nature_Neuroscience_2021/snake_workdir/Cortex_151507/figure/',
+            sample_name=name,
+            trait_name='GIANT_EUR_Height_2022_Nature',
+            fig_title='GIANT_EUR_Height_2022_Nature',
+            fig_height=800,
+            fig_width=800,
+            fig_style='light',
+            point_size=2,
+            annotation='annotation',
+        )
+        run_Visualize(config)
+    else:
+        parser = argparse.ArgumentParser(description="Visualization the results")
+        add_Visualization_args(parser)
+        args = parser.parse_args()
+        config = VisualizeConfig(**vars(args))
+
+        run_Visualize(config)

gsmap-1.60.dist-info/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2023 liyang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

gsmap-1.60.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: gsMap
+Version: 1.60
+Summary: Genetics-informed pathogenic spatial mapping
+Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Operating System :: POSIX :: Linux
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: tqdm
+Requires-Dist: progress
+Requires-Dist: pyyaml
+Requires-Dist: torch
+Requires-Dist: torch-geometric
+Requires-Dist: pyranges
+Requires-Dist: pyfiglet
+Requires-Dist: plotly
+Requires-Dist: kaleido
+Requires-Dist: sphinx ; extra == "doc"
+Requires-Dist: sphinx-argparse ; extra == "doc"
+Requires-Dist: sphinx-autobuild ; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
+Requires-Dist: sphinx-basic-ng ; extra == "doc"
+Requires-Dist: sphinx-charts ; extra == "doc"
+Requires-Dist: sphinx-copybutton ; extra == "doc"
+Requires-Dist: sphinx_inline_tabs ; extra == "doc"
+Requires-Dist: sphinx-markdown-tables ; extra == "doc"
+Requires-Dist: sphinx-rtd-theme ; extra == "doc"
+Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
+Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
+Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
+Requires-Dist: furo ; extra == "doc"
+Requires-Dist: myst-parser ; extra == "doc"
+Requires-Dist: nbsphinx ; extra == "doc"
+Project-URL: Documentation, https://...
+Project-URL: Home, https://github.com/LeonSong1995/gsMap
+Project-URL: Website, https://...
+Provides-Extra: doc
+
+# gsMap (genetically informed spatial mapping of cells for complex traits)
+[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/MeDuSA?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+
+## Features
+
+....
+
+## Installation
+
+install use pip:
+
+```bash
+pip install gsMap-mapping
+```
+
+install from source:
+
+```bash
+git clone
+cd gsMap-mapping
+pip install -e .
+```
+
+## Usage
+
+To use gsMap, navigate to the command line and enter `gsMap` followed by the subcommand that corresponds to the desired operation. Each subcommand may require specific arguments to run.
+
+### Basic Command Structure
+
+```bash
+gsMap subcommand [arguments...]
+```
+
+- `subcommand`: The specific operation you wish to perform.
+- `arguments`: The arguments and options required for the subcommand.
+
+### Available Subcommands
+
+(Provide a list and brief description of each available subcommand. For example:)
+
+- `run_find_latent_representations`: Finds latent representations using a GNN-VAE model.
+- `run_latent_to_gene`: Maps latent representations to gene markers.
+- `run_generate_ldscore`: Generates LD scores for genomic spots.
+- `run_spatial_ldsc`: Conducts spatial LDSC analysis.
+- `run_cauchy_combination`: Performs Cauchy combination tests for annotations.
+- `run_all_mode`: Executes a comprehensive pipeline covering all steps.
+
+### Examples
+
+To run a specific functionality, you need to provide the appropriate subcommand and arguments. For example:
+### Running Requirement
+
+
+```bash
+gsMap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
+```
+
+This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.
+
+## Contributing
+
+...
+
+## License
+
+....
+
+---
+

gsmap-1.60.dist-info/RECORD

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+gsMap/__init__.py,sha256=JxySn7SeLHZIin7_NnWdVJk6FCUs8Ov4Pttwn2fL4N0,78
+gsMap/__main__.py,sha256=jR-HT42Zzfj2f-7kFJy0bkWjNxcV1MyfQHXFpef2nSE,62
+gsMap/cauchy_combination_test.py,sha256=WI71HmSJ38Q2VEohnVrWHL02MnY0clqX9Fb5VrXCCz4,6758
+gsMap/config.py,sha256=2-gQR-nJRI9XfxegGCuUYMPDf43nuo7gWXR8JhtKWjs,39578
+gsMap/find_latent_representation.py,sha256=liRXtQKixYwGA6ZQmfXXVeHAypobACYO1wYT-wyr3AU,8337
+gsMap/format_sumstats.py,sha256=wC8eSFCbD8qpq5JOaxhYP5iL3JZ6NmG-JPThyQ52tDM,13838
+gsMap/generate_ldscore.py,sha256=s2nhq9MvQa6wfRRsCe93lv54zyimvNn1aW0-dG-PsXo,25494
+gsMap/generate_r2_matrix.py,sha256=BGe4WrCm19nQwzYz5vmNIC7tfIM2_QUMPd8JdfFDock,29761
+gsMap/jackknife.py,sha256=nEDPVQJOPQ_uqfUCGX_v5cQwokgCqUmJTT_8rVFuIQo,18244
+gsMap/latent_to_gene.py,sha256=lvEokL3po0kTnMk7mQvBwN0gkfO26myudRRQX1pX0BQ,11269
+gsMap/main.py,sha256=ttGY1uSmHaC6R1fPfuvonr3Nj5lZt_U3UFw15VQKDIM,1511
+gsMap/make_annotations.py,sha256=QhI3aTO9eOUuqvDXLe23eUGjld7bt_1H6vtvWX5TR5Y,23984
+gsMap/regression_read.py,sha256=ATfUapl4zypkUwo8xivzD7aGlZNSMavR-xVavSsmVkI,8780
+gsMap/spatial_ldsc_multiple_sumstats.py,sha256=Ixt8HpWZyJ7L1OA539mkvykdIDoZG9VT9ivwRmCOSwA,14440
+gsMap/visualize.py,sha256=FMuSInYfNZQMLHgh-jjER4j-U78SQVNCZJOTnL-xhgM,5645
+gsMap/GNN_VAE/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gsMap/GNN_VAE/adjacency_matrix.py,sha256=0-qw5qHGrGugkjgVyWLYjC0Qa_iKvR1TnFxAgCaxJFw,3500
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+gsMap/GNN_VAE/train.py,sha256=cAj81gJ9AwV-f5gqS1PjNtfkcZ1s_TtRcDIPIb4AtoM,3389
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+gsmap-1.60.dist-info/LICENSE,sha256=Ni2F-lLSv_H1xaVT3CoSrkiKzMvlgwh-dq8PE1esGyI,1094
+gsmap-1.60.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+gsmap-1.60.dist-info/METADATA,sha256=GelXw8zrDlZivWoHXDgMlKNk_abULmj15KQ9skrJTog,3940
+gsmap-1.60.dist-info/RECORD,,

gsmap-1.60.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: flit 3.9.0
+Root-Is-Purelib: true
+Tag: py3-none-any

gsmap-1.60.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+gsMap=gsMap.main:main
+