added test cases
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Florian Förster
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docs/lang_main/render/cytoscape.html
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docs/lang_main/render/cytoscape.html
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</head>
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<body>
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<main>
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<article id="content">
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<header>
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<h1 class="title">Module <code>lang_main.render.cytoscape</code></h1>
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</header>
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<section id="section-intro">
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</section>
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<section>
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</section>
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<section>
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</section>
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<section>
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<h2 class="section-title" id="header-functions">Functions</h2>
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<dl>
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<dt id="lang_main.render.cytoscape.analyse_network"><code class="name flex">
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<span>def <span class="ident">analyse_network</span></span>(<span>property_degree_weighted: str = 'degree_weighted',<br>network_name: str = 'token_graph') ‑> None</span>
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</code></dt>
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<dd>
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<details class="source">
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<summary>
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<span>Expand source code</span>
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</summary>
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<pre><code class="python">def analyse_network(
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property_degree_weighted: str = PROPERTY_NAME_DEGREE_WEIGHTED,
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network_name: str = CYTO_BASE_NETWORK_NAME,
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) -> None:
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node_table = p4c.get_table_columns(table='node', network=network_name)
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net_analyse_possible: bool = True
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if len(node_table) < 4: # pragma: no cover
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net_analyse_possible = False
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if net_analyse_possible:
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p4c.analyze_network(directed=False)
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node_table = p4c.get_table_columns(table='node', network=network_name)
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node_table['stress_norm'] = node_table['Stress'] / node_table['Stress'].max()
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node_table[CYTO_SELECTION_PROPERTY] = (
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node_table[property_degree_weighted]
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* node_table['BetweennessCentrality']
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* node_table['stress_norm']
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)
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else: # pragma: no cover
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node_table[CYTO_SELECTION_PROPERTY] = 1
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p4c.load_table_data(node_table, data_key_column='name', network=network_name)</code></pre>
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</details>
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<div class="desc"></div>
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</dd>
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<dt id="lang_main.render.cytoscape.apply_style_to_network"><code class="name flex">
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<span>def <span class="ident">apply_style_to_network</span></span>(<span>style_name: str = 'lang_main',<br>pth_to_stylesheet: pathlib.Path = WindowsPath('A:/Arbeitsaufgaben/lang-main/src/lang_main/cytoscape_config/lang_main.xml'),<br>network_name: str = 'token_graph',<br>node_size_property: str = 'node_selection',<br>min_node_size: int = 15,<br>max_node_size: int = 40,<br>sandbox_name: str = 'lang_main') ‑> None</span>
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</code></dt>
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<dd>
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||||
<details class="source">
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<summary>
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<span>Expand source code</span>
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</summary>
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<pre><code class="python">def apply_style_to_network(
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style_name: str = CYTO_STYLESHEET_NAME,
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pth_to_stylesheet: Path = CYTO_PATH_STYLESHEET,
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network_name: str = CYTO_BASE_NETWORK_NAME,
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node_size_property: str = CYTO_SELECTION_PROPERTY,
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min_node_size: int = 15,
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max_node_size: int = 40,
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sandbox_name: str = CYTO_SANDBOX_NAME,
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) -> None:
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"""Cytoscape: apply a chosen Cytoscape style to the defined network
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Parameters
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----------
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style_name : str, optional
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Cytoscape name of the style which should be applied,
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by default CYTO_STYLESHEET_NAME
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pth_to_stylesheet : Path, optional
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path where the stylesheet definition in Cytoscape's XML format can
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be found,
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by default CYTO_PATH_STYLESHEET
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network_name : str, optional
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network to apply the style on, by default CYTO_BASE_NETWORK_NAME
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Raises
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------
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FileNotFoundError
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if provided stylesheet can not be found under the provided path
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"""
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logger.debug('Applying style to network...')
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styles_avail = cast(list[str], p4c.get_visual_style_names())
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logger.debug('Available styles: %s', styles_avail)
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if style_name not in styles_avail:
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if not pth_to_stylesheet.exists():
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# existence for standard path verified at import, but not for other
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# provided paths
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raise FileNotFoundError(
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f'Visual stylesheet for Cytoscape not found under: >>{pth_to_stylesheet}<<'
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)
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# send to sandbox
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sandbox_filename = pth_to_stylesheet.name
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p4c.sandbox_send_to(
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source_file=pth_to_stylesheet,
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dest_file=sandbox_filename,
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overwrite=True,
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sandbox_name=sandbox_name,
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||||
)
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# load stylesheet
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p4c.import_visual_styles(sandbox_filename)
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p4c.set_visual_style(style_name, network=network_name)
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# node size mapping, only if needed property is available
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scheme = p4c.scheme_c_number_continuous(
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start_value=min_node_size, end_value=max_node_size
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)
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node_size_map = p4c.gen_node_size_map(
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node_size_property,
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number_scheme=scheme,
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mapping_type='c',
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style_name=style_name,
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default_number=min_node_size,
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)
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p4c.set_node_size_mapping(**node_size_map)
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fit_content(network_name=network_name)
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logger.debug('Style application to network successful.')</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: apply a chosen Cytoscape style to the defined network</p>
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||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>style_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>Cytoscape name of the style which should be applied,
|
||||
by default CYTO_STYLESHEET_NAME</dd>
|
||||
<dt><strong><code>pth_to_stylesheet</code></strong> : <code>Path</code>, optional</dt>
|
||||
<dd>path where the stylesheet definition in Cytoscape's XML format can
|
||||
be found,
|
||||
by default CYTO_PATH_STYLESHEET</dd>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network to apply the style on, by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
</dl>
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||||
<h2 id="raises">Raises</h2>
|
||||
<dl>
|
||||
<dt><code>FileNotFoundError</code></dt>
|
||||
<dd>if provided stylesheet can not be found under the provided path</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.build_subnetworks"><code class="name flex">
|
||||
<span>def <span class="ident">build_subnetworks</span></span>(<span>nodes_to_analyse: Iterable[int],<br>network_name: str = 'token_graph',<br>export_image: bool = True,<br>target_folder: pathlib.Path = WindowsPath('A:/Arbeitsaufgaben/lang-data/out')) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def build_subnetworks(
|
||||
nodes_to_analyse: Iterable[CytoNodeID],
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
export_image: bool = True,
|
||||
target_folder: Path = SAVE_PATH_FOLDER,
|
||||
) -> None:
|
||||
"""Cytoscape: iteratively build subnetworks from a collection of nodes
|
||||
and their respective neighbouring nodes
|
||||
|
||||
Parameters
|
||||
----------
|
||||
nodes_to_analyse : Iterable[CytoNodeID]
|
||||
collection of nodes to make subnetworks from, for each node a dedicated
|
||||
subnetwork will be generated
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||||
network_name : str, optional
|
||||
network which contains the provided nodes,
|
||||
by default CYTO_BASE_NETWORK_NAME
|
||||
export_image : bool, optional
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||||
trigger image export of newly generated subnetworks, by default True
|
||||
"""
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||||
logger.debug('Generating all subnetworks for node selection...')
|
||||
for idx, node in enumerate(nodes_to_analyse):
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select_neighbours_of_node(node=node, network_name=network_name)
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||||
make_subnetwork(
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||||
index=idx,
|
||||
network_name=network_name,
|
||||
export_image=export_image,
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||||
target_folder=target_folder,
|
||||
)
|
||||
logger.debug('Generation of all subnetworks for node selection successful.')</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: iteratively build subnetworks from a collection of nodes
|
||||
and their respective neighbouring nodes</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>nodes_to_analyse</code></strong> : <code>Iterable[CytoNodeID]</code></dt>
|
||||
<dd>collection of nodes to make subnetworks from, for each node a dedicated
|
||||
subnetwork will be generated</dd>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network which contains the provided nodes,
|
||||
by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
<dt><strong><code>export_image</code></strong> : <code>bool</code>, optional</dt>
|
||||
<dd>trigger image export of newly generated subnetworks, by default True</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.change_default_layout"><code class="name flex">
|
||||
<span>def <span class="ident">change_default_layout</span></span>(<span>) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def change_default_layout() -> None:
|
||||
"""Cytoscape: resets the default layout to `grid` to accelerate the import process
|
||||
(grid layout one of the fastest)
|
||||
|
||||
Raises
|
||||
------
|
||||
RequestException
|
||||
API endpoint not reachable or CyREST operation not successful
|
||||
"""
|
||||
body: dict[str, str] = {'value': 'grid', 'key': 'layout.default'}
|
||||
try:
|
||||
p4c.cyrest_put('properties/cytoscape3.props/layout.default', body=body)
|
||||
except RequestException as error:
|
||||
logger.error('[CytoAPIConnection] Property change of default layout not successful.')
|
||||
raise error</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: resets the default layout to <code>grid</code> to accelerate the import process
|
||||
(grid layout one of the fastest)</p>
|
||||
<h2 id="raises">Raises</h2>
|
||||
<dl>
|
||||
<dt><code>RequestException</code></dt>
|
||||
<dd>API endpoint not reachable or CyREST operation not successful</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.export_network_to_image"><code class="name flex">
|
||||
<span>def <span class="ident">export_network_to_image</span></span>(<span>filename: str,<br>target_folder: pathlib.Path = WindowsPath('A:/Arbeitsaufgaben/lang-data/out'),<br>filetype: Literal['JPEG', 'PDF', 'PNG', 'PS', 'SVG'] = 'SVG',<br>network_name: str = 'token_graph',<br>pdf_export_page_size: Literal['A0', 'A1', 'A2', 'A3', 'A4', 'A5', 'Auto', 'Legal', 'Letter', 'Tabloid'] = 'A4',<br>sandbox_name: str = 'lang_main') ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def export_network_to_image(
|
||||
filename: str,
|
||||
target_folder: Path = SAVE_PATH_FOLDER,
|
||||
filetype: CytoExportFileTypes = 'SVG',
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
pdf_export_page_size: CytoExportPageSizes = 'A4',
|
||||
sandbox_name: str = CYTO_SANDBOX_NAME,
|
||||
) -> None:
|
||||
"""Cytoscape: export current selected view as image
|
||||
|
||||
Parameters
|
||||
----------
|
||||
filename : str
|
||||
export filename
|
||||
filetype : CytoExportFileTypes, optional
|
||||
export filetype supported by Cytoscape, by default 'SVG'
|
||||
network_name : str, optional
|
||||
network to export, by default CYTO_BASE_NETWORK_NAME
|
||||
pdf_export_page_size : CytoExportPageSizes, optional
|
||||
page size which should be used for PDF exports supported by Cytoscape,
|
||||
by default 'A4'
|
||||
"""
|
||||
logger.debug('Exporting image to file...')
|
||||
if not target_folder.exists(): # pragma: no cover
|
||||
target_folder.mkdir(parents=True)
|
||||
dst_file_pth = (target_folder / filename).with_suffix(f'.{filetype.lower()}')
|
||||
|
||||
text_as_font = True
|
||||
if filetype == 'SVG':
|
||||
text_as_font = False
|
||||
|
||||
# close non-necessary windows and fit graph in frame before image display
|
||||
fit_content(network_name=network_name)
|
||||
# image is generated in sandbox directory and transferred to target destination
|
||||
# (preparation for remote instances of Cytoscape)
|
||||
p4c.export_image(
|
||||
filename=filename,
|
||||
type=filetype,
|
||||
network=network_name,
|
||||
overwrite_file=True,
|
||||
all_graphics_details=True,
|
||||
export_text_as_font=text_as_font,
|
||||
page_size=pdf_export_page_size,
|
||||
)
|
||||
logger.debug('Exported image to sandbox.')
|
||||
logger.debug('Transferring image from sandbox to target destination...')
|
||||
sandbox_filename = f'{filename}.{filetype.lower()}'
|
||||
p4c.sandbox_get_from(
|
||||
source_file=sandbox_filename,
|
||||
dest_file=str(dst_file_pth),
|
||||
overwrite=True,
|
||||
sandbox_name=sandbox_name,
|
||||
)
|
||||
logger.debug('Transfer of image from sandbox to target destination successful.')</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: export current selected view as image</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>filename</code></strong> : <code>str</code></dt>
|
||||
<dd>export filename</dd>
|
||||
<dt><strong><code>filetype</code></strong> : <code>CytoExportFileTypes</code>, optional</dt>
|
||||
<dd>export filetype supported by Cytoscape, by default 'SVG'</dd>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network to export, by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
<dt><strong><code>pdf_export_page_size</code></strong> : <code>CytoExportPageSizes</code>, optional</dt>
|
||||
<dd>page size which should be used for PDF exports supported by Cytoscape,
|
||||
by default 'A4'</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.fit_content"><code class="name flex">
|
||||
<span>def <span class="ident">fit_content</span></span>(<span>zoom_factor: float = 0.96, network_name: str = 'token_graph') ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def fit_content(
|
||||
zoom_factor: float = CYTO_NETWORK_ZOOM_FACTOR,
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
) -> None:
|
||||
p4c.hide_all_panels()
|
||||
p4c.fit_content(selected_only=False, network=network_name)
|
||||
zoom_current = p4c.get_network_zoom(network=network_name)
|
||||
zoom_new = zoom_current * zoom_factor
|
||||
p4c.set_network_zoom_bypass(zoom_new, bypass=False, network=network_name)</code></pre>
|
||||
</details>
|
||||
<div class="desc"></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.get_subgraph_node_selection"><code class="name flex">
|
||||
<span>def <span class="ident">get_subgraph_node_selection</span></span>(<span>network_name: str = 'token_graph', num_subgraphs: int = 5) ‑> list[int]</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def get_subgraph_node_selection(
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
num_subgraphs: int = CYTO_NUMBER_SUBGRAPHS,
|
||||
) -> list[CytoNodeID]:
|
||||
"""Cytoscape: obtain the relevant nodes for iterative subgraph generation
|
||||
|
||||
Parameters
|
||||
----------
|
||||
network_name : str, optional
|
||||
network to retrieve the nodes from, by default CYTO_BASE_NETWORK_NAME
|
||||
property_degree_weighted : str, optional
|
||||
property name which contains the weighted degree,
|
||||
by default PROPERTY_NAME_DEGREE_WEIGHTED
|
||||
num_subgraphs : int, optional
|
||||
number of relevant nodes which form the basis to generate subgraphs from,
|
||||
by default CYTO_NUMBER_SUBGRAPHS
|
||||
|
||||
Returns
|
||||
-------
|
||||
list[CytoNodeID]
|
||||
list containing all relevant Cytoscape nodes
|
||||
"""
|
||||
logger.debug('Selecting nodes for subgraph generation...')
|
||||
node_table = p4c.get_table_columns(table='node', network=network_name)
|
||||
node_table = node_table.sort_values(by=CYTO_SELECTION_PROPERTY, ascending=False)
|
||||
p4c.load_table_data(node_table, data_key_column='name', network=network_name)
|
||||
node_table_choice = node_table.iloc[:num_subgraphs]
|
||||
logger.debug('Selection of nodes for subgraph generation successful.')
|
||||
|
||||
return node_table_choice['SUID'].to_list()</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: obtain the relevant nodes for iterative subgraph generation</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network to retrieve the nodes from, by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
<dt><strong><code>property_degree_weighted</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>property name which contains the weighted degree,
|
||||
by default PROPERTY_NAME_DEGREE_WEIGHTED</dd>
|
||||
<dt><strong><code>num_subgraphs</code></strong> : <code>int</code>, optional</dt>
|
||||
<dd>number of relevant nodes which form the basis to generate subgraphs from,
|
||||
by default CYTO_NUMBER_SUBGRAPHS</dd>
|
||||
</dl>
|
||||
<h2 id="returns">Returns</h2>
|
||||
<dl>
|
||||
<dt><code>list[CytoNodeID]</code></dt>
|
||||
<dd>list containing all relevant Cytoscape nodes</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.import_to_cytoscape"><code class="name flex">
|
||||
<span>def <span class="ident">import_to_cytoscape</span></span>(<span>graph: networkx.classes.digraph.DiGraph | networkx.classes.graph.Graph,<br>network_name: str = 'token_graph',<br>sandbox_name: str = 'lang_main',<br>reinitialise_sandbox: bool = True) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def import_to_cytoscape(
|
||||
graph: DiGraph | Graph,
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
sandbox_name: str = CYTO_SANDBOX_NAME,
|
||||
reinitialise_sandbox: bool = True,
|
||||
) -> None:
|
||||
"""Cytoscape: import NetworkX graph as new network collection
|
||||
|
||||
Parameters
|
||||
----------
|
||||
graph : DiGraph | Graph
|
||||
NetworkX graph object
|
||||
"""
|
||||
logger.debug('Checking Cytoscape connection...')
|
||||
verify_connection()
|
||||
logger.debug('Checking graph size for rendering...')
|
||||
verify_graph_render_size(graph)
|
||||
logger.debug('Setting default layout to improve import speed...')
|
||||
change_default_layout()
|
||||
logger.debug('Setting Cytoscape sandbox...')
|
||||
p4c.sandbox_set(
|
||||
sandbox_name=sandbox_name,
|
||||
reinitialize=reinitialise_sandbox,
|
||||
copy_samples=False,
|
||||
)
|
||||
logger.debug('Importing to and analysing network in Cytoscape...')
|
||||
p4c.delete_all_networks()
|
||||
p4c.create_network_from_networkx(
|
||||
graph,
|
||||
title=network_name,
|
||||
collection=CYTO_COLLECTION_NAME,
|
||||
)
|
||||
analyse_network(network_name=network_name)
|
||||
logger.debug('Import and analysis of network to Cytoscape successful.')</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: import NetworkX graph as new network collection</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>graph</code></strong> : <code>DiGraph | Graph</code></dt>
|
||||
<dd>NetworkX graph object</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.layout_network"><code class="name flex">
|
||||
<span>def <span class="ident">layout_network</span></span>(<span>layout_name: Literal['attribute-circle', 'attribute-grid', 'attributes-layout', 'circular', 'cose', 'degree-circle', 'force-directed', 'force-directed-cl', 'fruchterman-rheingold', 'grid', 'hierarchical', 'isom', 'kamada-kawai', 'stacked-node-layout'] = 'force-directed',<br>layout_properties: dict[str, float | bool] = {'numIterations': 1000, 'defaultSpringCoefficient': 0.0001, 'defaultSpringLength': 45, 'defaultNodeMass': 11, 'isDeterministic': True, 'singlePartition': False},<br>network_name: str = 'token_graph') ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def layout_network(
|
||||
layout_name: CytoLayouts = CYTO_LAYOUT_NAME,
|
||||
layout_properties: CytoLayoutProperties = CYTO_LAYOUT_PROPERTIES,
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
) -> None:
|
||||
"""Cytoscape: apply a supported layout algorithm to currently selected
|
||||
network
|
||||
|
||||
Parameters
|
||||
----------
|
||||
layout_name : CytoLayouts, optional
|
||||
layout algorithm supported by Cytoscape (name of the CyREST API, does not
|
||||
necessarily match the name in the Cytoscape UI),
|
||||
by default CYTO_LAYOUT_NAME
|
||||
layout_properties : CytoLayoutProperties, optional
|
||||
configuration of parameters for the given layout algorithm,
|
||||
by default CYTO_LAYOUT_PROPERTIES
|
||||
network_name : str, optional
|
||||
network to apply the layout algorithm on, by default CYTO_BASE_NETWORK_NAME
|
||||
"""
|
||||
logger.debug('Applying layout to network...')
|
||||
p4c.set_layout_properties(layout_name, layout_properties)
|
||||
p4c.layout_network(layout_name=layout_name, network=network_name)
|
||||
fit_content(network_name=network_name)
|
||||
logger.debug('Layout application to network successful.')</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: apply a supported layout algorithm to currently selected
|
||||
network</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>layout_name</code></strong> : <code>CytoLayouts</code>, optional</dt>
|
||||
<dd>layout algorithm supported by Cytoscape (name of the CyREST API, does not
|
||||
necessarily match the name in the Cytoscape UI),
|
||||
by default CYTO_LAYOUT_NAME</dd>
|
||||
<dt><strong><code>layout_properties</code></strong> : <code>CytoLayoutProperties</code>, optional</dt>
|
||||
<dd>configuration of parameters for the given layout algorithm,
|
||||
by default CYTO_LAYOUT_PROPERTIES</dd>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network to apply the layout algorithm on, by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.make_subnetwork"><code class="name flex">
|
||||
<span>def <span class="ident">make_subnetwork</span></span>(<span>index: int,<br>network_name: str = 'token_graph',<br>export_image: bool = True,<br>target_folder: pathlib.Path = WindowsPath('A:/Arbeitsaufgaben/lang-data/out')) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def make_subnetwork(
|
||||
index: int,
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
export_image: bool = True,
|
||||
target_folder: Path = SAVE_PATH_FOLDER,
|
||||
) -> None:
|
||||
"""Cytoscape: generate a new subnetwork based on the currently
|
||||
selected nodes and edges
|
||||
|
||||
Parameters
|
||||
----------
|
||||
index : int
|
||||
id-like property to identify the subnetwork relative to its parent
|
||||
network_name : str, optional
|
||||
network to generate subnetwork from, by default CYTO_BASE_NETWORK_NAME
|
||||
export_image : bool, optional
|
||||
trigger image export of newly generated subnetwork, by default True
|
||||
"""
|
||||
logger.debug('Generating subnetwork with index %d...', index)
|
||||
subnetwork_name = network_name + f'_sub_{index+1}'
|
||||
p4c.create_subnetwork(
|
||||
nodes='selected',
|
||||
edges='selected',
|
||||
subnetwork_name=subnetwork_name,
|
||||
network=network_name,
|
||||
)
|
||||
p4c.set_current_network(subnetwork_name)
|
||||
|
||||
if export_image:
|
||||
time.sleep(1)
|
||||
export_network_to_image(
|
||||
filename=subnetwork_name,
|
||||
target_folder=target_folder,
|
||||
network_name=subnetwork_name,
|
||||
)
|
||||
|
||||
logger.debug('Generation of subnetwork with index %d successful.', index)</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: generate a new subnetwork based on the currently
|
||||
selected nodes and edges</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>index</code></strong> : <code>int</code></dt>
|
||||
<dd>id-like property to identify the subnetwork relative to its parent</dd>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network to generate subnetwork from, by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
<dt><strong><code>export_image</code></strong> : <code>bool</code>, optional</dt>
|
||||
<dd>trigger image export of newly generated subnetwork, by default True</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.reset_current_network_to_base"><code class="name flex">
|
||||
<span>def <span class="ident">reset_current_network_to_base</span></span>(<span>) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def reset_current_network_to_base() -> None:
|
||||
"""resets to currently selected network in Cytoscape back to the base one"""
|
||||
p4c.set_current_network(CYTO_BASE_NETWORK_NAME)</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>resets to currently selected network in Cytoscape back to the base one</p></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.select_neighbours_of_node"><code class="name flex">
|
||||
<span>def <span class="ident">select_neighbours_of_node</span></span>(<span>node: int, neighbour_iter_depth: int = 2, network_name: str = 'token_graph') ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def select_neighbours_of_node(
|
||||
node: CytoNodeID,
|
||||
neighbour_iter_depth: int = CYTO_ITER_NEIGHBOUR_DEPTH,
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
) -> None:
|
||||
"""Cytoscape: iterative selection of a node's neighbouring nodes and
|
||||
their connecting edges
|
||||
|
||||
Parameters
|
||||
----------
|
||||
node : CytoNodeID
|
||||
node which neighbours should be selected
|
||||
neighbour_iter_depth : int, optional
|
||||
indicates how many levels of neighbours should be choosen, e.g. 1 --> only
|
||||
first-level neighbours are considered which are directly connected to the node,
|
||||
2 --> all nodes with iteration depth of 1 are chosen and additionally their
|
||||
direct neighbours,
|
||||
by default CYTO_ITER_NEIGHBOUR_DEPTH
|
||||
network_name : str, optional
|
||||
network to perform action on, by default CYTO_BASE_NETWORK_NAME
|
||||
"""
|
||||
logger.debug('Selecting node neighbours for %s...', node)
|
||||
p4c.clear_selection(network=network_name)
|
||||
p4c.select_nodes(node, network=network_name)
|
||||
|
||||
for _ in range(neighbour_iter_depth):
|
||||
_ = p4c.select_first_neighbors(network=network_name)
|
||||
|
||||
_ = p4c.select_edges_connecting_selected_nodes()
|
||||
logger.debug('Selection of node neighbours for %s successful.', node)</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: iterative selection of a node's neighbouring nodes and
|
||||
their connecting edges</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>node</code></strong> : <code>CytoNodeID</code></dt>
|
||||
<dd>node which neighbours should be selected</dd>
|
||||
<dt><strong><code>neighbour_iter_depth</code></strong> : <code>int</code>, optional</dt>
|
||||
<dd>indicates how many levels of neighbours should be choosen, e.g. 1 –> only
|
||||
first-level neighbours are considered which are directly connected to the node,
|
||||
2 –> all nodes with iteration depth of 1 are chosen and additionally their
|
||||
direct neighbours,
|
||||
by default CYTO_ITER_NEIGHBOUR_DEPTH</dd>
|
||||
<dt><strong><code>network_name</code></strong> : <code>str</code>, optional</dt>
|
||||
<dd>network to perform action on, by default CYTO_BASE_NETWORK_NAME</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.verify_connection"><code class="name flex">
|
||||
<span>def <span class="ident">verify_connection</span></span>(<span>) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def verify_connection() -> None:
|
||||
"""Cytoscape: checks if CyREST and Cytoscape versions are compatible nad
|
||||
if Cytoscape API endpoint is reachable
|
||||
|
||||
Raises
|
||||
------
|
||||
CyError
|
||||
incompatible CyREST or Cytoscape versions
|
||||
RequestException
|
||||
API endpoint not reachable
|
||||
"""
|
||||
try:
|
||||
p4c.cytoscape_ping()
|
||||
except CyError as error: # pragma: no cover
|
||||
logger.error('[CyError] CyREST or Cytoscape version not supported.')
|
||||
raise error
|
||||
except RequestException as error:
|
||||
logger.error('[CytoAPIConnection] Connection to CyREST API failed.')
|
||||
raise error</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>Cytoscape: checks if CyREST and Cytoscape versions are compatible nad
|
||||
if Cytoscape API endpoint is reachable</p>
|
||||
<h2 id="raises">Raises</h2>
|
||||
<dl>
|
||||
<dt><code>CyError</code></dt>
|
||||
<dd>incompatible CyREST or Cytoscape versions</dd>
|
||||
<dt><code>RequestException</code></dt>
|
||||
<dd>API endpoint not reachable</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.verify_graph_render_size"><code class="name flex">
|
||||
<span>def <span class="ident">verify_graph_render_size</span></span>(<span>graph: networkx.classes.digraph.DiGraph | networkx.classes.graph.Graph,<br>max_node_count: int | None = 500,<br>max_edge_count: int | None = 800) ‑> None</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def verify_graph_render_size(
|
||||
graph: Graph | DiGraph,
|
||||
max_node_count: int | None = CYTO_MAX_NODE_COUNT,
|
||||
max_edge_count: int | None = CYTO_MAX_EDGE_COUNT,
|
||||
) -> None:
|
||||
"""verify that the graph size can still be handled within an acceptable time
|
||||
frame for rendering in Cytoscape
|
||||
|
||||
Parameters
|
||||
----------
|
||||
graph : Graph | DiGraph
|
||||
graph to verify
|
||||
max_node_count : int | None, optional
|
||||
maximum allowed number of nodes, by default CYTO_MAX_NODE_COUNT
|
||||
max_edge_count : int | None, optional
|
||||
maximum allowed number of edges, by default CYTO_MAX_EDGE_COUNT
|
||||
|
||||
Raises
|
||||
------
|
||||
GraphRenderError
|
||||
if any of the provided limits is exceeded
|
||||
"""
|
||||
num_nodes = len(graph.nodes)
|
||||
num_edges = len(graph.edges)
|
||||
if max_node_count is not None and num_nodes > max_node_count:
|
||||
raise GraphRenderError(
|
||||
f'Maximum number of nodes for rendering exceeded. '
|
||||
f'Limit {max_node_count}, Counted: {num_nodes}'
|
||||
)
|
||||
|
||||
if max_edge_count is not None and num_edges > max_edge_count:
|
||||
raise GraphRenderError(
|
||||
f'Maximum number of edges for rendering exceeded. '
|
||||
f'Limit {max_edge_count}, Counted: {num_edges}'
|
||||
)</code></pre>
|
||||
</details>
|
||||
<div class="desc"><p>verify that the graph size can still be handled within an acceptable time
|
||||
frame for rendering in Cytoscape</p>
|
||||
<h2 id="parameters">Parameters</h2>
|
||||
<dl>
|
||||
<dt><strong><code>graph</code></strong> : <code>Graph | DiGraph</code></dt>
|
||||
<dd>graph to verify</dd>
|
||||
<dt><strong><code>max_node_count</code></strong> : <code>int | None</code>, optional</dt>
|
||||
<dd>maximum allowed number of nodes, by default CYTO_MAX_NODE_COUNT</dd>
|
||||
<dt><strong><code>max_edge_count</code></strong> : <code>int | None</code>, optional</dt>
|
||||
<dd>maximum allowed number of edges, by default CYTO_MAX_EDGE_COUNT</dd>
|
||||
</dl>
|
||||
<h2 id="raises">Raises</h2>
|
||||
<dl>
|
||||
<dt><code>GraphRenderError</code></dt>
|
||||
<dd>if any of the provided limits is exceeded</dd>
|
||||
</dl></div>
|
||||
</dd>
|
||||
<dt id="lang_main.render.cytoscape.verify_table_property"><code class="name flex">
|
||||
<span>def <span class="ident">verify_table_property</span></span>(<span>property: str,<br>table_type: Literal['node', 'edge', 'network'] = 'node',<br>network_name: str = 'token_graph') ‑> bool</span>
|
||||
</code></dt>
|
||||
<dd>
|
||||
<details class="source">
|
||||
<summary>
|
||||
<span>Expand source code</span>
|
||||
</summary>
|
||||
<pre><code class="python">def verify_table_property(
|
||||
property: str,
|
||||
table_type: Literal['node', 'edge', 'network'] = 'node',
|
||||
network_name: str = CYTO_BASE_NETWORK_NAME,
|
||||
) -> bool:
|
||||
table = p4c.get_table_columns(table=table_type, network=network_name)
|
||||
logger.debug('Table >>%s<< wiht columns: %s', table, table.columns)
|
||||
|
||||
return property in table.columns</code></pre>
|
||||
</details>
|
||||
<div class="desc"></div>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section>
|
||||
</section>
|
||||
</article>
|
||||
<nav id="sidebar">
|
||||
<div class="toc">
|
||||
<ul></ul>
|
||||
</div>
|
||||
<ul id="index">
|
||||
<li><h3>Super-module</h3>
|
||||
<ul>
|
||||
<li><code><a title="lang_main.render" href="index.html">lang_main.render</a></code></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><h3><a href="#header-functions">Functions</a></h3>
|
||||
<ul class="">
|
||||
<li><code><a title="lang_main.render.cytoscape.analyse_network" href="#lang_main.render.cytoscape.analyse_network">analyse_network</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.apply_style_to_network" href="#lang_main.render.cytoscape.apply_style_to_network">apply_style_to_network</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.build_subnetworks" href="#lang_main.render.cytoscape.build_subnetworks">build_subnetworks</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.change_default_layout" href="#lang_main.render.cytoscape.change_default_layout">change_default_layout</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.export_network_to_image" href="#lang_main.render.cytoscape.export_network_to_image">export_network_to_image</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.fit_content" href="#lang_main.render.cytoscape.fit_content">fit_content</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.get_subgraph_node_selection" href="#lang_main.render.cytoscape.get_subgraph_node_selection">get_subgraph_node_selection</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.import_to_cytoscape" href="#lang_main.render.cytoscape.import_to_cytoscape">import_to_cytoscape</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.layout_network" href="#lang_main.render.cytoscape.layout_network">layout_network</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.make_subnetwork" href="#lang_main.render.cytoscape.make_subnetwork">make_subnetwork</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.reset_current_network_to_base" href="#lang_main.render.cytoscape.reset_current_network_to_base">reset_current_network_to_base</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.select_neighbours_of_node" href="#lang_main.render.cytoscape.select_neighbours_of_node">select_neighbours_of_node</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.verify_connection" href="#lang_main.render.cytoscape.verify_connection">verify_connection</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.verify_graph_render_size" href="#lang_main.render.cytoscape.verify_graph_render_size">verify_graph_render_size</a></code></li>
|
||||
<li><code><a title="lang_main.render.cytoscape.verify_table_property" href="#lang_main.render.cytoscape.verify_table_property">verify_table_property</a></code></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</nav>
|
||||
</main>
|
||||
<footer id="footer">
|
||||
<p>Generated by <a href="https://pdoc3.github.io/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc</cite> 0.11.5</a>.</p>
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||||
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|
||||
</body>
|
||||
</html>
|
||||
Reference in New Issue
Block a user