NaviCell-class: NaviCell reference class

In sysbio-curie/RNaviCell: Visualization of High-Throughput Data on Large-Scale Biological Networks

Description

NaviCell (https://navicell.curie.fr) is a web-based environment for browsing, commenting and analyzing very large biological molecular networks using Google Maps and for visualizing 'omics' data on top of the network maps.

Details

NaviCell can also act as a server allowing to be remotely controlled through a REST API. A python and a R language bindings have been developped on top of the REST API to hide technical details and to provide users and programmers a friendly interface. A Java binding has been initiated.

This is the R binding implementation. For more information about the NaviCell Web Service and a tutorial on how to use it, see https://navicell.curie.fr/pages/nav_web_service.html and https://github.com/eb00/RNaviCell.

Methods

attachLastSession(...)

Attach NaviCell handle to the last existing NaviCell Web Service session.

attachSession(session_id)

Attach a NaviCell server session ID.

barplotEditorApply(...)

Apply changes for the barplot editor.

barplotEditorApplyAndClose(...)

Apply changes and close the barplot editor.

barplotEditorCancel(...)

Cancel changes and close the barplot editor.

barplotEditorClearSamples(...)

Clear all samples in the barplot editor.

barplotEditorClose(...)

Close the barplot editor.

barplotEditorOpen(...)

Open the barplot editor.

barplotEditorSelectAllGroups(...)

Select all groups in the barplot editor.

barplotEditorSelectAllSamples(...)

Select all samples in the barplot editor.

barplotEditorSelectDatatable(datatable_name)

Select a datatable in the barplot editor.

barplotEditorSelectSample(col_num, sample_name)

Select a sample or a group in the barplot editor. col_num = column index number, sample_name = sample or group name

barplotEditorSetTransparency(value)

Select transparency parameter in the barplot editor. value = integer between 1 and 100

continuousConfigApply(datatable_name, parameter_type)

Apply changes to the continuous configuration editor. parameter_type = 'size' or 'shape' or 'color'.

continuousConfigApplyAndClose(datatable_name, datatable_parameter)

Apply changes and close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

continuousConfigCancelAndClose(datatable_name, datatable_parameter)

Cancel changes and close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

continuousConfigClose(datatable_name, datatable_parameter)

Close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

continuousConfigOpen(datatable_name, datatable_parameter)

Open continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

continuousConfigSetAbsVal(datatable_parameter, datatable_name, checked)

Set absolute value mode for continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size', checked = TRUE or FALSE.

continuousConfigSetColorAt(datatable_name, sample_or_group, index, color_hex_value)

Set continuous configuration color value. sample_or_group = 'sample' or 'group'.

continuousConfigSetGroupMethod(datatable_parameter, datatable_name, method_index)

Set the method used when multiple symbols map to the same entity. datatable_parameter = 'shape' or 'color' or 'size', method_index = integer.

continuousConfigSetSampleMethod(datatable_parameter, datatable_name, method_index)

Set the method used when multiple symbols map to the same entity. datatable_parameter = 'shape' or 'color' or 'size', method_index = integer.

continuousConfigSetSelectionShape(datatable_name, sample_or_group, index, shape)

Set the shape selection to a given value for the 'shape' parameter. sample_or_group = 'sample' or 'group', index = integer, shape = integer.

continuousConfigSetSelectionSize(datatable_name, sample_or_group, index, size)

Set the size selection to a given value for the 'size' parameter. sample_or_group = 'sample' or 'group', index = integer, size = integer.

continuousConfigSetStepCount(sample_or_group, datatable_parameter, datatable_name, step_count)

Set continuous configuration step count parameter to a given value. sample_or_group = 'sample' or 'group'. parameter = 'shape' or 'color' or 'size' step_count = integer value.

continuousConfigSetValueAt(datatable_name, parameter_type, sample_or_group, index, continuous_value)

Set continuous configuration continuous value at a given index. sample_or_group = 'sample' or 'group'. parameter_type = 'size' or 'shape' or 'color'.

continuousConfigSwitchGroupTab(datatable_name, datatable_parameter)

Switch continuous configuration editor window to 'group' tab. Parameter = 'shape' or 'color' or 'size'.

continuousConfigSwitchSampleTab(datatable_name, datatable_parameter)

Switch continuous configuration editor window to 'sample' tab. Parameter = 'shape' or 'color' or 'size'.

drawingConfigApply(...)

Apply changes to drawing configuration dialog.

drawingConfigApplyAndClose(...)

Apply changes to drawing configuration and close dialog.

drawingConfigCancel(...)

Cancel changes to drawing configuration dialog.

drawingConfigClose(...)

Close drawing configuration dialog.

drawingConfigOpen(...)

Open drawing configuration dialog.

drawingConfigSelectBarplot(checked)

Select barplot display in drawing configuration dialog. checked = TRUE or FALSE.

drawingConfigSelectDisplayAllGenes(...)

Select 'Display all genes' option in drawing configuration dialog.

drawingConfigSelectDisplaySelectedGenes(...)

Select 'Display selected genes' option in drawing configuration dialog.

drawingConfigSelectGlyph(glyph_num, checked)

Select glyph display in drawing configuration dialog. glyph_num = glyph number, checked = TRUE or FALSE.

drawingConfigSelectHeatmap(checked)

Select heatmap display in drawing configuration dialog. checked = TRUE or FALSE.

drawingConfigSelectMapStaining(checked)

Select map staining display in drawing configuration dialog. checked = TRUE or FALSE.

file2dataString(fileName)

Load the content of a text file as tab-delimited string. Convert to NaviCell compatible format.

findEntities(entity, bubble)

Find one or more entities on the map. entity = entity's name pattern (string), bubble = TRUE or FALSE.

formatJson(list_param)

Format list of parameters to NaviCell server compatible JSON format (internal utility).

formatResponse(response)

Format response obtained from the RCurl 'postForm' command (internal utility).

geneList2string(gene_list)

Convert a gene list R object to a formatted string (internal utility).

generateSessionId(...)

Generate a session ID.

getBiotypeList(...)

Return the list of biotypes understood by NaviCell Web Service.

getHugoList(...)

Get the list of the HUGO gene symbols for the current map (the list is stored in the object field hugo_list.

getImportedDatatables(...)

Return the list of datatables imported in the current NaviCell session.

getImportedGenes(...)

Return the list of genes from all the datatables imported in the current NaviCell session.

getImportedSamples(...)

Return the list of samples from all the datatables imported in the current NaviCell session.

getModuleList(...)

Return the module list of the current NaviCell map.

glyphEditorApply(glyph_num)

Apply changes in the glyph editor.

glyphEditorApplyAndClose(glyph_num)

Apply changes and close the glyph editor.

glyphEditorCancel(glyph_num)

Cancel changes and close the glyph editor.

glyphEditorClose(glyph_num)

Close the glyph editor.

glyphEditorOpen(glyph_num)

Open the glyph editor. glyph_num = glyph number

glyphEditorSelectColorDatatable(glyph_num, datatable_name)

Select datatable for glyph color in the glyph editor.

glyphEditorSelectSample(glyph_num, sample_name)

Select sample or group in the glyph editor.

glyphEditorSelectShapeDatatable(glyph_num, datatable_name)

Select datatable for glyph shape in the glyph editor.

glyphEditorSelectSizeDatatable(glyph_num, datatable_name)

Select datatable for glyph size in the glyph editor.

glyphEditorSetTransparency(glyph_num, value)

Set transparency parameter in the glyph editor. value = integer between 1 and 100.

heatmapEditorApply(...)

Apply changes for the heatmap editor.

heatmapEditorApplyAndClose(...)

Apply changes and close the heatmap editor.

heatmapEditorCancel(...)

Cancel changes and close the heatmap editor.

heatmapEditorClearSamples(...)

Clear all samples in heatmap editor.

heatmapEditorClose(...)

Close the heatmap editor.

heatmapEditorOpen(...)

Open the heatmap editor.

heatmapEditorSelectAllGroups(...)

Select all groups in heatmap editor.

heatmapEditorSelectAllSamples(...)

Select all samples in heatmap editor.

heatmapEditorSelectDatatable(row_num, datatable_name)

Select datatable in heatmap editor. row_num = editor row number.

heatmapEditorSelectSample(col_num, sample_name)

Select sample or group in heatmap editor. col_num = editor column number, sample_name = sample or group name.

heatmapEditorSetTransparency(value)

Set transparency parameter in heatmap editor. value = integer between 1 and 100.

importDatatable(datatable_biotype, datatable_name, mat)

Import a datatable (matrix) in the current map session.

incMessageId(...)

Increase message ID counter.

isImported(...)

Test if data table is imported (internal utility).

launchBrowser(...)

Launch client browser and points to the default NaviCell map.

listSessions(...)

List all NaviCell server sessions.

makeData(json_string)

Create NaviCell server command string from a list of parameters (internal utility).

mapStainingEditorApply(...)

Apply modifications for the map staining editor.

mapStainingEditorApplyAndClose(...)

Apply changes and close the map staining editor.

mapStainingEditorCancel(...)

Cancel modifications and close the map staining editor.

mapStainingEditorClose(...)

Close the map staining editor.

mapStainingEditorOpen(...)

Open the map staining editor.

mapStainingEditorSelectDatatable(datatable_name)

Select a datatable for the map staining editor.

mapStainingEditorSelectSample(sample_name)

Select a sample for the map staining editor.

mapStainingEditorSetTransparency(transparency_value)

Set the transparency value parameter for the map staining editor (integer value between 1 and 100).

matrix2string(mat)

Convert an R matrix object to a formatted string (internal utility).

moveMapCenter(x, y)

Move the map center (relative). x = x coordinate (integer), y = y coordinate (integer).

mydataDialogClose(...)

Close MyData Dialog.

mydataDialogOpen(...)

Open MyData Dialog.

mydataDialogSetDatatables(...)

Set Datatables tab active for MyData Dialog.

mydataDialogSetGenes(...)

Set Genes tab active for MyData Dialog.

mydataDialogSetGroups(...)

Set Groups tab active for MyData Dialog.

mydataDialogSetModules(...)

Set Modules tab active for MyData Dialog.

mydataDialogSetSamples(...)

Set Samples tab active for MyData Dialog.

readDatatable(fileName)

Read a data file and create an R matrix. Returns a matrix object.

sampleAnnotationApply(...)

Apply the modifications done on a sample annotation table.

sampleAnnotationCancel(...)

Cancel changes and close sample annotation dialog.

sampleAnnotationClose(...)

Close sample annotation dialog.

sampleAnnotationOpen(...)

Open sample annotation dialog.

sampleAnnotationSelectAnnotation(annotation_name, true_or_false)

Select or un-select an annotation for creating groups from a sample annotation table. true_or_false = TRUE, select, true_or_false = FALSE, un-select.

selectEntity(entity)

Select an entity on the map. entity = entity's name (string)

sendBigData(fill_cmd)

slice data in packets big data string and send it to server (internal utility)

serverIsReady(...)

Test if NaviCell server is ready (internal utility).

setMapCenter(location)

Set the relative position of the map center. location = 'MAP_CENTER' or 'MAP_EAST' or 'MAP_SOUTH' or MAP_NORTH' or 'MAP_SOUTH_WEST' or 'MAP_SOUTH_EAST' or 'MAP_NORTH_EAST'.

setMapCenterAbsolute(pos_x, pos_y)

Set the absolute position of the map center. x = x coordinate (integer), y = y coordinate (integer).

setZoom(zoom_level)

Set a given zoom level on associated NaviCell map in browser. zoom_level = integer value.

uncheckAllEntities(...)

Uncheck all entities on the map.

unhighlightAllEntities(...)

Uncheck all entities on the map.

unorderedConfigApply(datatable_name, datatable_parameter)

Apply changes to unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

unorderedConfigApplyAndClose(datatable_name, datatable_parameter)

Apply changes to unordered discrete configuration editor for a given type of parameter, and close the window. datatable_parameter = 'shape' or 'color' or 'size'.

unorderedConfigCancel(datatable_name, datatable_parameter)

Cancel changes for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

unorderedConfigClose(datatable_name, datatable_parameter)

Open unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

unorderedConfigOpen(datatable_name, datatable_parameter)

Open unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

unorderedConfigSetAdvancedConfig(datatable_name, datatable_parameter, checked)

Open/close advanced configuration for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'.

unorderedConfigSetDiscreteColor(datatable_name, sample_or_group, index, color)

Set color value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, color = string hex code color value, e.g. 'FF0000'.

unorderedConfigSetDiscreteCondition(datatable_name, datatable_parameter, sample_or_group, index, condition)

Set condition value for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'. sample_or_group = 'sample' or 'group', index = integer, condition = integer.

unorderedConfigSetDiscreteShape(datatable_name, sample_or_group, index, shape)

Set shape value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, shape = integer.

unorderedConfigSetDiscreteSize(datatable_name, sample_or_group, index, size)

Set size value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, size = integer.

unorderedConfigSetDiscreteValue(datatable_name, datatable_parameter, sample_or_group, index, value)

Set discrete value for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size', sample_or_group = 'sample' or 'group', index = integer, value = double.

unorderedConfigSwitchGroupTab(datatable_name, datatable_parameter)

Switch to group tab for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'.

unorderedConfigSwitchSampleTab(datatable_name, datatable_parameter)

Switch to sample tab for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'.

waitForImported(...)

Wait until data is imported (internal utility).

waitForReady(...)

Wait until NaviCell server is ready (internal utility).

Examples

## Not run: 
### Opens a communication with web service, build does not finish if example is tested
file<-system.file("extdata", "script.R", package = "RNaviCell")
source("file")

## End(Not run)

sysbio-curie/RNaviCell documentation built on May 31, 2019, 12:48 a.m.