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script.py
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script.py
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from curie.navicell import NaviCell, Options
# 1. Instantiate and set Options:
options = Options()
# options.proxy_url = 'http://localhost/navicell/proxy/nv_proxy.php'
# options.map_url = 'http://localhost/navicell/maps/e947a215-c865-416d-b21a-4d773c9ef5db/master/index.php'
#options.proxy_url = 'https://navicell.vincent-noel.fr/proxy/nv_proxy.php'
options.proxy_url = 'https://navicell.vincent-noel.fr/cgi-bin/nv_proxy.php'
options.map_url = 'https://navicell.vincent-noel.fr/maps/394c8f64-e940-4dfa-8258-acc1930f102a/master/index.php'
#options.proxy_url = 'https://navicell.vincent.science/cgi-bin/nv_proxy.php'
#options.map_url = 'https://navicell.vincent.science/navicell/newtest/maps/wikiproteinmap/master/index.php'
# options.proxy_url = 'http://localhost/proxy/nv_proxy.php'
# options.map_url = 'http://localhost/maps/ff4e9e8a-e2a9-467e-b6a5-560fa6e14aab/master/index.php'
# If you want to specify a particular Web Browser, you have to set options.browser_command, otherwise the default browser will be used.
# For instance, to use firefox on MacOS:
# options.browser_command = 'open -a Firefox %s'
# To use google chrome on Linux:
# options.browser_command = 'chromium-browser --allow-file-access-from-files %s'
# options.browser_command = 'firefox %s'
# options.browser_command = '/opt/firefox-developer/firefox-80.0b8/firefox/firefox %s'
# 2. Instantiate a NaviCell client handle
nv = NaviCell(options)
# 3. Launch browser
nv.launchBrowser()
# 4. Check hugo list
print("Getting hugo data...")
hugo_list = nv.getHugoList()
print(hugo_list)
print("Loading data...")
data = nv.makeDataFromFile("/home/vincent/Work/code/NaviCell/site/docroot/data/ovca_expression.txt")
print("Importing data...")
nv.importDatatables(data, "mRNAExpression", "mRNA expression data", {"open_drawing_editor": False, "import_display_markers": "checked", "import_display_heatmap": False})
print("Staining configuration")
nv.mapStainingEditorOpen('')
nv.mapStainingEditorSelectSample('', 'TCGA_04_1332')
nv.mapStainingEditorSelectDatatable('', 'mRNAExpression')
nv.mapStainingEditorSetTransparency('', 0.10)
nv.mapStainingEditorApplyAndClose('')
print("Zooming")
nv.setZoom('', 5)
nv.setCenter('', 'ABSOLUTE',95, -25)