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Methods defined here:
- __init__(self, options)
- Instantiate a NaviCell handle.
Args:
:param options(curie.navicell.Options): browser_commmand, proxy_url and map_url to be used.
Notices:
- options.map_url has to be set. options.browser_command and options.map_url can be set (respectively)
to False and empty string.
- options can be an instance of any class as soon as browser_commmand, proxy_url and
map_url attributes are provided. For instance, when used with nvpy, options is actually
an instance of optparse.Values.
- attachLastSession(self)
- Attach NaviCell handle to the last existing NaviCell Web Service session.
Action granted according to security conditions defined in the Web Service configuration.
- attachRefererSession(self, referer)
- Attach NaviCell handle to the last existing NaviCell Web Service session launched from
a given referer (IP client).
Action granted according to security conditions defined in the Web Service configuration.
Args:
:param referer(string): IP client address of the referer
- attachSession(self, session_id)
- Attach NaviCell handle to an existing NaviCell Web Service session.
Action granted according to security conditions defined in the Web Service configuration.
Args:
:param session_id(string): session ID to which NaviCell handle must be attached
- barplotEditorAllGroups(self, module)
- Select all groups in the barplot editor.
Similar to a click on the 'All Groups' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorAllSamples(self, module)
- Select all samples in the barplot editor.
Similar to a click on the 'All Samples' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorApply(self, module)
- Apply the changes in the barplot editor.
Similar to a click on the 'Apply' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorApplyAndClose(self, module)
- Apply the changes in the barplot editor and close the window.
Similar to a click on the 'OK' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorCancel(self, module)
- Cancel the changes in the barplot editor and close the window.
Similar to a click on the 'Cancel' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorClearSamples(self, module)
- Clear all samples and groups in the barplot editor.
Similar to a click on the 'Clear Samples' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorClose(self, module)
- Close the barplot editor.
Similar to a click on the 'Close' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorFromHeatmap(self, module)
- Report samples and groups selected in the heatmap editor to the barplot editor.
Similar to a click on the 'From Heatmap' button of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorOpen(self, module)
- Open the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- barplotEditorSelectDatatable(self, module, datatable)
- Select the datatable in the barplot editor.
Similar to a selection in the 'Select a datatable' list of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name to be selected.
- barplotEditorSelectSample(self, module, where, sample)
- Select a sample in the barplot editor.
Similar to a selection in a 'Select a sample' list of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param where (int): 0-based sample position in the barplot.
:param sample (string): sample name to be selected.
- barplotEditorSetTransparency(self, module, value)
- Set the transparency in the barplot editor.
Similar to a change of the transparency slider of the barplot editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param value (double): transparency value.
- clearSessions(self)
- Clear all active NaviCell Web Service sessions.
Action granted according to security conditions defined in the Web Service configuration.
- datatableConfigApply(self, module, datatable, config_type)
- Apply changes the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- datatableConfigApplyAndClose(self, module, datatable, config_type)
- Apply changes and close the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- datatableConfigCancel(self, module, datatable, config_type)
- Cancel changes and close the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- datatableConfigClose(self, module, datatable, config_type)
- Close the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- datatableConfigOpen(self, module, datatable, config_type)
- Open the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- datatableConfigSetColorAt(self, module, datatable, config_type, tabname, idx, color)
- Set color at a specified index in the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param tabname (string): tab name in the configuration dialog;
must be NaviCell.TABNAME_SAMPLES or NaviCell.TABNAME_GROUPS
:param idx (int): color index
:param color (string): hexa RGB color
- datatableConfigSetCondAt(self, module, datatable, config_type, tabname, idx, cond)
- Set condition at a specified index in the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param tabname (string): tab name in the configuration dialog;
must be NaviCell.TABNAME_SAMPLES or NaviCell.TABNAME_GROUPS
:param idx (int): condition index
:param shape (int): condition; must be NaviCell.COND_DISCRETE_IGNORE,
NaviCell.COND_DISCRETE_NO_ELEMENT, NaviCell.COND_DISCRETE_AT_LEAST_ONE_ELEMENT,
NaviCell.COND_DISCRETE_ALL_ELEMENTS or NaviCell.COND_DISCRETE_VALUE
- datatableConfigSetGroupAdvancedConfiguration(self, module, datatable, config_type, checked)
- Set group advanced configuration in the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param checked (boolean): set/unset advanced configuration
- datatableConfigSetGroupMethod(self, module, datatable, config_type, method)
- Set the group method of the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param method (int): method name; must be NaviCell.METHOD_CONTINUOUS_AVERAGE, NaviCell.METHOD_CONTINUOUS_MEDIAN,
NaviCell.METHOD_CONTINUOUS_MINVAL, NaviCell.METHOD_CONTINUOUS_MAXVAL, NaviCell.METHOD_CONTINUOUS_ABS_AVERAGE,
NaviCell.METHOD_CONTINUOUS_ABS_MINVAL or NaviCell.METHOD_CONTINUOUS_ABS_MAXVAL
- datatableConfigSetSampleAbsoluteValue(self, module, datatable, config_type, checked)
- Set the sample absolute value mode of the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param checked (boolean): set/unset sample absolute value mode
- datatableConfigSetSampleMethod(self, module, datatable, config_type, method)
- Set the sample method of the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param method (int): method name; must be NaviCell.METHOD_CONTINUOUS_AVERAGE, NaviCell.METHOD_CONTINUOUS_MEDIAN,
NaviCell.METHOD_CONTINUOUS_MINVAL, NaviCell.METHOD_CONTINUOUS_MAXVAL, NaviCell.METHOD_CONTINUOUS_ABS_AVERAGE,
NaviCell.METHOD_CONTINUOUS_ABS_MINVAL or NaviCell.METHOD_CONTINUOUS_ABS_MAXVAL
- datatableConfigSetShapeAt(self, module, datatable, config_type, tabname, idx, shape)
- Set shape at a specified index in the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param tabname (string): tab name in the configuration dialog;
must be NaviCell.TABNAME_SAMPLES or NaviCell.TABNAME_GROUPS
:param idx (int): shape index
:param shape (int): shape; must be NaviCell.SHAPE_TRIANGLE, NaviCell.SHAPE_SQUARE,
NaviCell.SHAPE_RECTANGLE, NaviCell.SHAPE_DIAMOND, NaviCell.SHAPE_HEXAGON or
NaviCell.SHAPE_CIRCLE
- datatableConfigSetSizeAt(self, module, datatable, config_type, tabname, idx, size)
- Set size at a specified index in the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param tabname (string): tab name in the configuration dialog;
must be NaviCell.TABNAME_SAMPLES or NaviCell.TABNAME_GROUPS
:param idx (int): size index
:param size (int): size value
- datatableConfigSetStepCount(self, module, datatable, config_type, tabname, step_count)
- Set the step count of the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param tabname (string): tab name in the configuration dialog;
must be NaviCell.TABNAME_SAMPLES or NaviCell.TABNAME_GROUPS
:param step_count (int): step count
- datatableConfigSetValueAt(self, module, datatable, config_type, tabname, idx, value)
- Set value at a specified index in the datatable configuration dialog for the given type.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
:param tabname (string): tab name in the configuration dialog;
must be NaviCell.TABNAME_SAMPLES or NaviCell.TABNAME_GROUPS
:param idx (int): value index
:param value (double): value
- datatableConfigSwitchGroupTab(self, module, datatable, config_type)
- Switch the datatable configuration dialog for the given type to the Groups tab.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- datatableConfigSwitchSampleTab(self, module, datatable, config_type)
- Switch the datatable configuration dialog for the given type to the Samples tab.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name
:param config_type (string): configuration type; must be NaviCell.CONFIG_COLOR,
NaviCell.CONFIG_SHAPE, NaviCell.CONFIG_SIZE or NaviCell.CONFIG_COLOR_SIZE
- drawingConfigApply(self, module)
- Apply the changes in the drawing configuration dialog.
Similar to a click on the 'Apply' button of the drawing configuration dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigApplyAndClose(self, module)
- Apply the changes in the drawing configuration dialog and close the window.
Similar to a click on the 'OK' button of the drawing configuration dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigCancel(self, module)
- Cancel the changes in the drawing configuration dialog and close the window.
Similar to a click on the 'Cancel' button of the drawing configuration dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigClose(self, module)
- Close the drawing configuration dialog.
Similar to a click on the 'Close' button of the drawing configuration dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigDisplayAllGenes(self, module)
- Will display DLOs for all genes.
Similar to the selection of the 'All Genes' checkbox in the 'Display DLOs' section
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigDisplaySelectedGenes(self, module)
- Will display DLOs for selected genes only.
Similar to the selection of the 'Selected Genes' checkbox in the 'Display DLOs' section.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigOpen(self, module)
- Open the drawing configuration dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- drawingConfigSelectBarplot(self, module, select=True)
- Select/unselect a barplot chart.
Similar to:
- a selection/unselection of the 'Display' checkbox in the 'Chart' section, and:
- a 'Barplot' selection/unselection in the 'Chart Type' list
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param select (boolean): select Barplot if True, unselect otherwise
- drawingConfigSelectGlyph(self, module, num, select=True)
- Select/unselect a given glyph.
Similar to a selection/unselection of one of the 'Display' checkbox in the 'Glyphs' section
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph number; valid values are 1 to 5.
:param select (boolean): select the Glyph if True, unselect otherwise
- drawingConfigSelectHeatmap(self, module, select=True)
- Select/unselect a heatmap chart.
Similar to:
- a selection/unselection of the 'Display' checkbox in the 'Chart' section, and:
- a 'Heatmap' selection/unselection in the 'Chart Type' list
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param select (boolean): select Heatmap if True, unselect otherwise
- drawingConfigSelectMapStaining(self, module, select=True)
- Select/unselect the map staining.
Similar to a selection/unselection of the 'Display' checkbox in the 'Map Staining' section
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param select (boolean): select Map Staining if True, unselect otherwise
- examples(self)
- Display some examples.
- executeCommands(self, module, commands)
- Execute a set of commands encoded in the NaviCell WS protocol.
- findEntities(self, module, pattern, hints={}, open_bubble=False)
- Find and select entities in the map.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param pattern (string): search pattern.
:param hints (map): hint modifier. Valid keys are in, class, op, token.
:param open_bubble (boolean): if True open associated bubbles, otherwise don't.
For instance:
findEntities('', 'rbx', {'token' : 'regex', 'in': 'label,tag,annot'}, True)
which is equivalent to:
findEntities('', 'rbx /token=regex;in=label,tag,annot', True)
Complete search syntax is as follows:
PATTERN [/MOD]
where PATTERN is a sequence of regular expressions
- if regex are separated by comma, OR search is performed
- if regex are separated by space, AND search is performed
where MOD is a semi-colon separated list of MOD_ITEM
where MOD_ITEM is under the form
in=label
in=tag
in=annot
in=all
token=word
token=regex
op=eq
op=neq
class=all
class=all_included
class=all_but_included
class=class_name,class_name,...
class!=class_name,class_name,...
Default is: /in=label;in=tag;token=word;op=eq;class=all_but_included
Examples:
rbx
xp rbx
xp,rbx
xp rbx /in=label
xp rbx /in=label;class=protein
xp rbx /class=protein,gene
xp rbx /class!=protein,gene
xp rbx /op=neq;in=label;class=protein,gene
xp rxb /token=regex;in=all
- getBiotypeList(self)
- Return the list of biotypes understood by NaviCell Web Service.
In the current version, the returned biotype list is as follows:
[{'name': 'mRNA expression data', 'subtype': 'CONTINUOUS', 'type': 'EXPRESSION'},
{'name': 'microRNA expression data', 'subtype': 'CONTINUOUS', 'type': 'EXPRESSION'},
{'name': 'Protein expression data', 'subtype': 'CONTINUOUS', 'type': 'EXPRESSION'},
{'name': 'Discrete Copy number data', 'subtype': 'ORDERED_DISCRETE', 'type': 'COPYNUMBER'},
{'name': 'Continuous copy number data', 'subtype': 'CONTINUOUS', 'type': 'COPYNUMBER'},
{'name': 'Mutation data', 'subtype': 'UNORDERED_DISCRETE', 'type': 'MUTATION'},
{'name': 'Gene list', 'subtype': 'SET', 'type': 'GENELIST'}]
- getCommandHistory(self, module)
- Get the command history of the NaviCell Web Service.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- getDatatableGeneList(self)
- Return the list of genes of the imported datatables which have been found in the map.
- getDatatableList(self)
- Return the datatables imported in the NaviCell map.
- getDatatableSampleList(self)
- Return the list of samples of the imported datatables.
- getHugoList(self)
- Return the list of HUGOs (gene names) of the NaviCell map.
- getModuleList(self)
- Return the module list of the NaviCell map.
For instance, the module list returned from the CellCycle map:
[{'name': 'E2F1', 'id': 'E2F1'},
{'name': 'P21CIP', 'id': 'P21CIP'},
{'name': 'CYCLIND', 'id': 'CYCLIND'},
{'name': 'CYCLINE', 'id': 'CYCLINE'},
{'name': 'E2F4', 'id': 'E2F4'},
{'name': 'E2F6', 'id': 'E2F6'},
{'name': 'CYCLINH', 'id': 'CYCLINH'},
{'name': 'RB', 'id': 'RB'},
{'name': 'INK4', 'id': 'INK4'},
{'name': 'P27KIP', 'id': 'P27KIP'},
{'name': 'APOPTOSIS_ENTRY', 'id': 'APOPTOSIS_ENTRY'},
{'name': 'WEE', 'id': 'WEE'},
{'name': 'CDC25', 'id': 'CDC25'},
{'name': 'CYCLINA', 'id': 'CYCLINA'},
{'name': 'CYCLINC', 'id': 'CYCLINC'},
{'name': 'CYCLINB', 'id': 'CYCLINB'},
{'name': 'APC', 'id': 'APC'}]
- getSessionId(self)
- Return the session ID.
- glyphEditorApply(self, module, num)
- Apply the changes in the glyph editor.
Similar to a click on the 'Apply' button of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
- glyphEditorApplyAndClose(self, module, num)
- Apply the changes in the glyph editor and close the window.
Similar to a click on the 'OK' button of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
- glyphEditorCancel(self, module, num)
- Cancel the changes in the glyph editor and close the window.
Similar to a click on the 'Cancel' button of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
- glyphEditorClose(self, module, num)
- Close the glyph editor.
Similar to a click on the 'Close' button of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
- glyphEditorOpen(self, module, num)
- Open the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
- glyphEditorSelectColorDatatable(self, module, num, datatable)
- Select the color datatable (eg. used to select a color) in the glyph editor.
Similar to a selection in the 'Select a datatable' Color list of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
:param datatable (string): datatable name to be selected.
- glyphEditorSelectSample(self, module, num, sample)
- Select a sample in the glyph editor.
Similar to a selection in the 'Select a sample' list of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
:param sample (string): sample name to be selected.
- glyphEditorSelectShapeDatatable(self, module, num, datatable)
- Select the shape datatable (eg. used to select a shape) in the glyph editor.
Similar to a selection in the 'Select a datatable' Shape list of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
:param datatable (string): datatable name to be selected.
- glyphEditorSelectSizeDatatable(self, module, num, datatable)
- Select the size datatable (eg. used to select a size) in the glyph editor.
Similar to a selection in the 'Select a datatable' Size list of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
:param datatable (string): datatable name to be selected.
- glyphEditorSetTransparency(self, module, num, value)
- Set the transparency in the glyph editor.
Similar to a change of the transparency slider of the glyph editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param num (int): glyph editor number; valid values are 1 to 5.
:param value (double): transparency value.
- heatmapEditorAllGroups(self, module)
- Select all groups in the heatmap editor.
Similar to a click on the 'All Groups' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorAllSamples(self, module)
- Select all samples in the heatmap editor.
Similar to a click on the 'All Samples' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorApply(self, module)
- Apply the changes in the heatmap editor.
Similar to a click on the 'Apply' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorApplyAndClose(self, module)
- Apply the changes in the heatmap editor and close the window.
Similar to a click on the 'OK' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorCancel(self, module)
- Cancel the changes in the heatmap editor and close the window.
Similar to a click on the 'Cancel' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorClearSamples(self, module)
- Clear all samples and groups in the heatmap editor.
Similar to a click on the 'Clear Samples' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorClose(self, module)
- Close the heatmap editor.
Similar to a click on the 'Close' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorFromBarplot(self, module)
- Report samples and groups selected in the barplot editor to the heatmap editor.
Similar to a click on the 'From Barplot' button of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorOpen(self, module)
- Open the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- heatmapEditorSelectDatatable(self, module, where, datatable)
- Select a datatable in the heatmap editor.
Similar to a selection in a 'Select a Datatable' list of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param where (int): 0-based datatable position in the heatmap.
:param datatable (string): datatable name to be selected.
- heatmapEditorSelectSample(self, module, where, sample)
- Select a sample in the heatmap editor.
Similar to a selection in a 'Select a sample' list of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param where (int): 0-based sample position in the heatmap.
:param sample (string): sample name to be selected.
- heatmapEditorSetTransparency(self, module, value)
- Set the transparency in the heatmap editor.
Similar to a change of the transparency slider of the heatmap editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param value (double): transparency value.
- importDatatables(self, datatable_url_or_data, datatable_name, datatable_biotype, params={})
- Import one or several datatables.
Args:
:param datatable_url_or_data (string): datatable(s) to be imported:
URL or data returned from makeData or makeDataFromFile expected.
:param datatable_name (string): name of the datatable that will appear in the NaviCell session.
:param datatable_biotype (string): biotype of the datatable file.
:param params (map): opening hints.
- launchBrowser(self)
- Launchs the client browser according to options given at NaviCell instantation.
- listSessions(self)
- Display all active NaviCell Web Service sessions.
Action granted according to security conditions defined in the Web Service configuration.
- makeAnnotationData(self, data)
- Builds a string suitable for NaviCell Web Service from a python sample/annotation matrix.
Matrix format:
- first line is: NAME word followed by a tab separated list of annotation names.
- each line begins with an sample name and must be followed by a tab separated list of
sample/annotation values.
- makeAnnotationDataFromFile(self, filename)
- Builds a string suitable for NaviCell Web Service from a python sample/annotation matrix contained in a file.
Matrix format:
- first line is: NAME word followed by a tab separated list of annotation names.
- each line begins with an sample name and must be followed by a tab separated list of
sample/annotation values.
- makeData(self, data)
- Builds a string suitable for NaviCell Web Service from a python matrix of gene/sample values.
Matrix format:
- first line is: GENE word followed by a tab separated list of sample names,
- each line begins with an gene name and must be followed by a tab separated list of gene/sample values.
Eliminates genes not present in the NaviCell map.
- makeDataFromFile(self, filename)
- Builds a string suitable for NaviCell Web Service from a matrix of gene/sample values contained in a file.
Matrix format:
- first line is: GENE word followed by a tab separated list of sample names,
- each line begins with an gene name and must be followed by a tab separated list of gene/sample values.
Eliminates genes not present in the NaviCell map.
- mapStainingEditorApply(self, module)
- Apply the changes in the map staining editor.
Similar to a click on the 'Apply' button of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- mapStainingEditorApplyAndClose(self, module)
- Apply the changes in the map staining editor and close the window.
Similar to a click on the 'OK' button of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- mapStainingEditorCancel(self, module)
- Cancel the changes in the map staining editor and close the window.
Similar to a click on the 'Cancel' button of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- mapStainingEditorClose(self, module)
- Close the map staining editor.
Similar to a click on the 'Close' button of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- mapStainingEditorOpen(self, module)
- Open the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- mapStainingEditorSelectDatatable(self, module, datatable)
- Select the datatable used for colors in the map staining editor.
Similar to a selection in the 'Select a datatable' Color list of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param datatable (string): datatable name to be selected.
- mapStainingEditorSelectSample(self, module, sample)
- Select the sample in the map staining editor.
Similar to a selection in the 'Select a sample' list of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param sample (string): sample name to be selected.
- mapStainingEditorSetTransparency(self, module, value)
- Set the transparency in the map staining editor.
Similar to a change of the transparency slider of the map staining editor.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param value (double): transparency value.
- myDataClose(self, module)
- Close the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- myDataOpen(self, module)
- Open the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- myDataSelectDatatableTab(self, module)
- Select the 'Datatable' Tab in the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- myDataSelectGeneTab(self, module)
- Select the 'Gene' Tab in the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- myDataSelectGroupTab(self, module)
- Select the 'Group' Tab in the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- myDataSelectModuleTab(self, module)
- Select the 'Module' Tab in the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- myDataSelectSampleTab(self, module)
- Select the 'Sample' Tab in the MyData dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- noticeClose(self, module)
- Close the notice dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- noticeMessage(self, module, header, msg, position='left top', width=0, height=0)
- Open the notice dialog and display a message.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param header (string): message header (title)
:param msg (string): html message
:param position (string): (optional) CSS position of the dialog, for instance 'left top', 'right top' etc.
:param width (int): (optional) width in pixel
:param height (int): (optional) height in pixel
- noticeOpen(self, module)
- Open the notice dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- openModule(self, module2open)
- Open a module.
This method works only under some conditions of the security configuration of the client browser (popup configuration).
Args:
:param module2open (string): module to be opened
- prepareImportDialog(self, module, filename, name, biotype)
- Fill the import dialog fields.
Data (datatable, gene list etc.) can then be imported by a user click on the Import button:
the import itself cannot be trigged from javascript for security reasons, that's why a user
action is required.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param filename (string): path of the data file
:param name (string): name of the data to be imported
:param biotype (string): biotype of the data file.
- reset(self)
- Resets the current session. NaviCell handle cannot communicate anymore with the Web Service.
- sampleAnnotationApply(self, module)
- Apply the changes in the sample annotation dialog.
Similar to a click on the 'Apply' button of the sample annotation dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- sampleAnnotationCancel(self, module)
- Cancel the changes in the sample annotation dialog and close the window.
Similar to a click on the 'Cancel' button of the sample annotation dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- sampleAnnotationClose(self, module)
- Close the sample annotation dialog.
Similar to a click on the 'Close' button of the sample annotation dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- sampleAnnotationImport(self, sample_annotation_url_or_data)
- Import the given annotation data or URL.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param sample_annotation_url_or_data (string): sample annotation to be imported:
URL or data returned from makeAnnotationData or makeAnnotationDataFromFile expected.
- sampleAnnotationOpen(self, module)
- Open the sample annotation dialog.
Args:
:param module (string): module on which to apply the command; empty string for current map.
- sampleAnnotationSelectAnnotation(self, module, annot, select=True)
- Select/unselect an annotation.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param annot (annot): annotation name
:param select (boolean): select annotation if True, unselect otherwise
- selectEntity(self, module, entity_name)
- Select a given entity.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param entity_name (string): name of the entity to be selected
- setCenter(self, module, where, lng=0, lat=0)
- Set the center of the map.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param where(string): the location of center, valid values are:
MAP_CENTER
MAP_NORTH
MAP_WEST
MAP_EAST
MAP_SOUTH
MAP_NORTH_WEST
MAP_NORTH_EAST
MAP_SOUTH_WEST
MAP_SOUTH_EAST
RELATIVE
ABSOLUTE
:param lng(double): longitude if center is set to RELATIVE or ABSOLUTE, ignored otherwise
:param lat(double): latitude if center is set to RELATIVE or ABSOLUTE, ignored otherwise
- setTrace(self, trace)
- For debug only. Activates / Desactivates traces according to the trace argument.
- setZoom(self, module, zoom)
- Set the zoom level of a map to a given level.
Args:
:param module (string): module on which to apply the command; empty string for current map.
:param zoom (int): zoom level.
- uncheckAllEntities(self, module)
- Unselect all entities in the map.
Args:
:param module (string): module on which to apply the command; empty string for current map.
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- COND_DISCRETE_ALL_ELEMENTS = 3
- COND_DISCRETE_AT_LEAST_ONE_ELEMENT = 2
- COND_DISCRETE_IGNORE = 0
- COND_DISCRETE_NO_ELEMENT = 1
- COND_DISCRETE_VALUE = 4
- CONFIG_COLOR = 'color'
- CONFIG_COLOR_SIZE = 'color_size'
- CONFIG_SHAPE = 'shape'
- CONFIG_SIZE = 'size'
- METHOD_CONTINUOUS_ABS_AVERAGE = 5
- METHOD_CONTINUOUS_ABS_MAXVAL = 7
- METHOD_CONTINUOUS_ABS_MINVAL = 6
- METHOD_CONTINUOUS_AVERAGE = 1
- METHOD_CONTINUOUS_MAXVAL = 4
- METHOD_CONTINUOUS_MEDIAN = 2
- METHOD_CONTINUOUS_MINVAL = 3
- SHAPE_CIRCLE = 5
- SHAPE_DIAMOND = 3
- SHAPE_HEXAGON = 4
- SHAPE_RECTANGLE = 2
- SHAPE_SQUARE = 1
- SHAPE_TRIANGLE = 0
- TABNAME_GROUPS = 'group'
- TABNAME_SAMPLES = 'sample'
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