gsMap 1.67__py3-none-any.whl → 1.71__py3-none-any.whl

gsMap/visualize.py

@@ -1,199 +1,199 @@
-from pathlib import Path
-from typing import Literal
-
-import numpy as np
-import pandas as pd
-import plotly.express as px
-import scanpy as sc
-from scipy.spatial import KDTree
-
-from gsMap.config import VisualizeConfig
-
-
-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, feature_series: pd.Series, annotation):
-    spot_name = adata.obs_names.to_list()
-    assert 'spatial' in adata.obsm.keys(), 'spatial coordinates are not found in adata.obsm'
-
-    # to DataFrame
-    space_coord = adata.obsm['spatial']
-    if isinstance(space_coord, np.ndarray):
-        space_coord = pd.DataFrame(space_coord, columns=['sx', 'sy'], index=spot_name)
-    else:
-        space_coord = pd.DataFrame(space_coord.values, columns=['sx', 'sy'], index=spot_name)
-
-    space_coord = space_coord[space_coord.index.isin(feature_series.index)]
-    space_coord_concat = pd.concat([space_coord.loc[feature_series.index], feature_series], 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 estimate_point_size_for_plot(coordinates, DEFAULT_PIXEL_WIDTH = 1000):
-    tree = KDTree(coordinates)
-    distances, _ = tree.query(coordinates, k=2)
-    avg_min_distance = np.mean(distances[:, 1])
-    # get the width and height of the plot
-    width = np.max(coordinates[:, 0]) - np.min(coordinates[:, 0])
-    height = np.max(coordinates[:, 1]) - np.min(coordinates[:, 1])
-
-    scale_factor = DEFAULT_PIXEL_WIDTH / max(width, height)
-    pixel_width = width * scale_factor
-    pixel_height = height * scale_factor
-
-    point_size = np.ceil(avg_min_distance * scale_factor)
-    return (pixel_width, pixel_height), point_size
-
-
-def draw_scatter(space_coord_concat, title=None, fig_style: Literal['dark', 'light'] = 'light',
-                 point_size: int = None, width=800, height=600, annotation=None, color_by='logp'):
-    # Set theme based on fig_style
-    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.reverse()
-
-    # Create the scatter plot
-    fig = px.scatter(
-        space_coord_concat,
-        x='sx',
-        y='sy',
-        color=color_by,
-        symbol='annotation' if annotation is not None else None,
-        title=title,
-        color_continuous_scale=custom_color_scale,
-        range_color=[0, max(space_coord_concat[color_by])],
-    )
-
-    # Update marker size if specified
-    if point_size is not None:
-        fig.update_traces(marker=dict(size=point_size, symbol='circle'))
-
-    # Update layout for figure size
-    fig.update_layout(
-        autosize=False,
-        width=width,
-        height=height,
-    )
-
-    # Adjusting the legend
-    fig.update_layout(
-        legend=dict(
-            yanchor="top",
-            y=0.95,
-            xanchor="left",
-            x=1.0,
-            font=dict(
-                size=10,
-            )
-        )
-    )
-
-    # Update colorbar to be at the bottom and horizontal
-    fig.update_layout(
-        coloraxis_colorbar=dict(
-            orientation='h',  # Make the colorbar horizontal
-            x=0.5,  # Center the colorbar horizontally
-            y=-0.0,  # Position below the plot
-            xanchor='center',  # Anchor the colorbar at the center
-            yanchor='top',  # Anchor the colorbar at the top to keep it just below the plot
-            len=0.75,  # Length of the colorbar relative to the plot width
-            title=dict(
-                text='-log10(p)' if color_by == 'logp' else color_by,  # Colorbar title
-                side='top'  # Place the title at the top of the colorbar
-            )
-        )
-    )
-    # Remove gridlines, axis labels, and ticks
-    fig.update_xaxes(
-        showgrid=False,   # Hide x-axis gridlines
-        zeroline=False,   # Hide x-axis zero line
-        showticklabels=False,  # Hide x-axis tick labels
-        title=None,       # Remove x-axis title
-        scaleanchor='y',  # Link the x-axis scale to the y-axis scale
-    )
-
-    fig.update_yaxes(
-        showgrid=False,   # Hide y-axis gridlines
-        zeroline=False,   # Hide y-axis zero line
-        showticklabels=False,  # Hide y-axis tick labels
-        title=None        # Remove y-axis title
-    )
-
-    # Adjust margins to ensure no clipping and equal axis ratio
-    fig.update_layout(
-        margin=dict(l=0, r=0, t=20, b=10),  # Adjust margins to prevent clipping
-        height=width  # Ensure the figure height matches the width for equal axis ratio
-    )
-
-    # Adjust the title location and font size
-    fig.update_layout(
-        title=dict(
-            y=0.98,
-            x=0.5,  # Center the title horizontally
-            xanchor='center',  # Anchor the title at the center
-            yanchor='top',  # Anchor the title at the top
-            font=dict(
-                size=20  # Increase the title font size
-            )
-        ))
-
-    return fig
-
-
-
-def run_Visualize(config: VisualizeConfig):
-    print(f'------Loading LDSC results of {config.ldsc_save_dir}...')
-    ldsc = load_ldsc(ldsc_input_file=Path(config.ldsc_save_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.hdf5_with_latent_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
-                       )
-
-
-    # Visualization
-    output_dir = Path(config.output_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'
-    output_file_csv = output_dir / f'{config.sample_name}_{config.trait_name}.csv'
-
-    fig.write_html(str(output_file_html))
-    fig.write_image(str(output_file_pdf))
-    space_coord_concat.to_csv(str(output_file_csv))
-
-    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}.')
+from pathlib import Path
+from typing import Literal
+
+import numpy as np
+import pandas as pd
+import plotly.express as px
+import scanpy as sc
+from scipy.spatial import KDTree
+
+from gsMap.config import VisualizeConfig
+
+
+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, feature_series: pd.Series, annotation):
+    spot_name = adata.obs_names.to_list()
+    assert 'spatial' in adata.obsm.keys(), 'spatial coordinates are not found in adata.obsm'
+
+    # to DataFrame
+    space_coord = adata.obsm['spatial']
+    if isinstance(space_coord, np.ndarray):
+        space_coord = pd.DataFrame(space_coord, columns=['sx', 'sy'], index=spot_name)
+    else:
+        space_coord = pd.DataFrame(space_coord.values, columns=['sx', 'sy'], index=spot_name)
+
+    space_coord = space_coord[space_coord.index.isin(feature_series.index)]
+    space_coord_concat = pd.concat([space_coord.loc[feature_series.index], feature_series], 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 estimate_point_size_for_plot(coordinates, DEFAULT_PIXEL_WIDTH = 1000):
+    tree = KDTree(coordinates)
+    distances, _ = tree.query(coordinates, k=2)
+    avg_min_distance = np.mean(distances[:, 1])
+    # get the width and height of the plot
+    width = np.max(coordinates[:, 0]) - np.min(coordinates[:, 0])
+    height = np.max(coordinates[:, 1]) - np.min(coordinates[:, 1])
+
+    scale_factor = DEFAULT_PIXEL_WIDTH / max(width, height)
+    pixel_width = width * scale_factor
+    pixel_height = height * scale_factor
+
+    point_size = np.ceil(avg_min_distance * scale_factor)
+    return (pixel_width, pixel_height), point_size
+
+
+def draw_scatter(space_coord_concat, title=None, fig_style: Literal['dark', 'light'] = 'light',
+                 point_size: int = None, width=800, height=600, annotation=None, color_by='logp'):
+    # Set theme based on fig_style
+    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.reverse()
+
+    # Create the scatter plot
+    fig = px.scatter(
+        space_coord_concat,
+        x='sx',
+        y='sy',
+        color=color_by,
+        symbol='annotation' if annotation is not None else None,
+        title=title,
+        color_continuous_scale=custom_color_scale,
+        range_color=[0, max(space_coord_concat[color_by])],
+    )
+
+    # Update marker size if specified
+    if point_size is not None:
+        fig.update_traces(marker=dict(size=point_size, symbol='circle'))
+
+    # Update layout for figure size
+    fig.update_layout(
+        autosize=False,
+        width=width,
+        height=height,
+    )
+
+    # Adjusting the legend
+    fig.update_layout(
+        legend=dict(
+            yanchor="top",
+            y=0.95,
+            xanchor="left",
+            x=1.0,
+            font=dict(
+                size=10,
+            )
+        )
+    )
+
+    # Update colorbar to be at the bottom and horizontal
+    fig.update_layout(
+        coloraxis_colorbar=dict(
+            orientation='h',  # Make the colorbar horizontal
+            x=0.5,  # Center the colorbar horizontally
+            y=-0.0,  # Position below the plot
+            xanchor='center',  # Anchor the colorbar at the center
+            yanchor='top',  # Anchor the colorbar at the top to keep it just below the plot
+            len=0.75,  # Length of the colorbar relative to the plot width
+            title=dict(
+                text='-log10(p)' if color_by == 'logp' else color_by,  # Colorbar title
+                side='top'  # Place the title at the top of the colorbar
+            )
+        )
+    )
+    # Remove gridlines, axis labels, and ticks
+    fig.update_xaxes(
+        showgrid=False,   # Hide x-axis gridlines
+        zeroline=False,   # Hide x-axis zero line
+        showticklabels=False,  # Hide x-axis tick labels
+        title=None,       # Remove x-axis title
+        scaleanchor='y',  # Link the x-axis scale to the y-axis scale
+    )
+
+    fig.update_yaxes(
+        showgrid=False,   # Hide y-axis gridlines
+        zeroline=False,   # Hide y-axis zero line
+        showticklabels=False,  # Hide y-axis tick labels
+        title=None        # Remove y-axis title
+    )
+
+    # Adjust margins to ensure no clipping and equal axis ratio
+    fig.update_layout(
+        margin=dict(l=0, r=0, t=20, b=10),  # Adjust margins to prevent clipping
+        height=width  # Ensure the figure height matches the width for equal axis ratio
+    )
+
+    # Adjust the title location and font size
+    fig.update_layout(
+        title=dict(
+            y=0.98,
+            x=0.5,  # Center the title horizontally
+            xanchor='center',  # Anchor the title at the center
+            yanchor='top',  # Anchor the title at the top
+            font=dict(
+                size=20  # Increase the title font size
+            )
+        ))
+
+    return fig
+
+
+
+def run_Visualize(config: VisualizeConfig):
+    print(f'------Loading LDSC results of {config.ldsc_save_dir}...')
+    ldsc = load_ldsc(ldsc_input_file=Path(config.ldsc_save_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.hdf5_with_latent_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
+                       )
+
+
+    # Visualization
+    output_dir = Path(config.output_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'
+    output_file_csv = output_dir / f'{config.sample_name}_{config.trait_name}.csv'
+
+    fig.write_html(str(output_file_html))
+    fig.write_image(str(output_file_pdf))
+    space_coord_concat.to_csv(str(output_file_csv))
+
+    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}.')
     print(f'------The visualization data is saved in a csv file: {output_file_csv}.')

{gsmap-1.67.dist-info → gsmap-1.71.dist-info}/LICENSE

@@ -1,21 +1,21 @@
-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.
+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-1.67.dist-info → gsmap-1.71.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gsMap
-Version: 1.67
+Version: 1.71
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.8
@@ -18,7 +18,6 @@ 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
@@ -52,30 +51,38 @@ 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://yanglab.westlake.edu.cn/gsmap/document
+Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
 Project-URL: Home, https://github.com/LeonSong1995/gsMap
 Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
 Provides-Extra: doc
 
-# gsMap (genetically informed spatial mapping of cells for complex traits)
-[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/gsMap?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
-[![pypi-badge](https://img.shields.io/pypi/v/gsMap)](https://pypi.org/p/gsMap)
-[![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![GitHub Stars](https://img.shields.io/github/stars/LeonSong1995/gsMap?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![PyPI Version](https://img.shields.io/pypi/v/gsMap)](https://pypi.org/project/gsMap)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-![Model architecture](schematic.png)
+## Introduction
 
-## 1.Citation
-Liyang Song, Wenhao Chen, Junren Hou, Minmin Guo, Jian Yang (2024) Spatially resolved mapping of cells associated with human complex traits. (Under review)
+`gsMap` (genetically informed spatial mapping of cells for complex traits) integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.
 
-## 2.Installation
 
-install use pip:
+## Key Features
+- **Spatially-aware High-Resolution Trait Mapping**
+- **Spatial Region Identification**
+- **Putative Causal Genes Identification**
+
+![Model Architecture](schematic.png)
+
+## Installation
+
+Install using pip:
 
 ```bash
+conda create -n gsMap python>3.8
+conda activate gsMap
 pip install gsMap
 ```
 
-install from source:
+Install from source:
 
 ```bash
 git clone https://github.com/LeonSong1995/gsMap.git
@@ -83,17 +90,16 @@ cd gsMap
 pip install -e .
 ```
 
-## 3.Usage
-
-Please checkout the documentations and tutorials at
-[gsMap.docs](https://yanglab.westlake.edu.cn/gsmap/document).
-
+Verify the installation by running the following command:
+```bash
+gsmap --help
+```
 
-## 4.Online visualization
+## Usage
 
-To visualize the traits-embryo or traits-brain association spatial maps, please refer to [gsmap.visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
+Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
 
-....
+## Online Visualization
 
----
+To visualize the traits-cell association spatial maps, please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
 

gsmap-1.71.dist-info/RECORD

@@ -0,0 +1,31 @@
+gsMap/__init__.py,sha256=xwuyVm3wc8MEgSfC3D0LNmecSOC2bkVXYWf0cpwX3I0,74
+gsMap/__main__.py,sha256=Ih3PPSJezd9UpmkdfH1PXYYecCpk6hkQF039BQU1ocs,60
+gsMap/cauchy_combination_test.py,sha256=jMXNKWajI5NSmKeKu5PVJMYMtiApL6ZeYrSOSqC-ESU,5553
+gsMap/config.py,sha256=2U_KNlrENMh6XFRJWn88CCOe2unctWYehyUshHt9LU0,40362
+gsMap/diagnosis.py,sha256=SUbEXqEPfziSrbytxNnH7hiNypocyCOAYPeUYDwgPHw,12947
+gsMap/find_latent_representation.py,sha256=h3douGRcrkyNrWEieNnwzc4dXacySx_VMAPZrn2wKyg,4460
+gsMap/format_sumstats.py,sha256=vPJD5qdqd_CjHw5MkihYpSMLcDx7wsNySsmoXRElaW0,13439
+gsMap/generate_ldscore.py,sha256=s0evdoGJ2QKZYMxHGm_z01yf7yE6RWa1iUOJzSh-OZY,28471
+gsMap/latent_to_gene.py,sha256=W7icT8o7GjUwrnHyNgdPFTCr03T6w8fB8vbApg1i-So,9452
+gsMap/main.py,sha256=b3pLWvc70UlO24QXW9Zl7Nd7rlErxlQSM5Y_RqwcNNM,1254
+gsMap/report.py,sha256=pr7K8zEyunun5LHzRtLBaoLjsw8-PfdbJWKMvsTxoj0,6803
+gsMap/run_all_mode.py,sha256=fXO5QNZbkQpQjkZTznqq5Ct1OihIRiFb4iwGHtnEryA,8194
+gsMap/setup.py,sha256=eOoPalGAHTY06_7a35nvbOaKQhq0SBE5GK4pc4bp3wc,102
+gsMap/spatial_ldsc_multiple_sumstats.py,sha256=Pc4MtsLilZZVtCVhQWaxePEyVj6tXva1VWQ2oRZOFRA,18011
+gsMap/visualize.py,sha256=pLp8iyh0L7UU405LfpjEgbGuKbf19_4YyMHZWo6wE7M,7255
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