NaviCell REST API

 Version 1.1.3
 April 2015

 Institut Curie, 26 rue d'Ulm - 75005 Paris

Introduction

NaviCell is a web-based environment for browsing and commenting very large molecular networks using Google Maps and for visualizing omics data on top of the network maps.

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 a user's friendly interface. A Java binding has been initiated.

This document introduces the NaviCell REST API. The audience is developpers wanting to write a binding for other languages such as Ruby, Perl or whatever.

To illustrate the REST API, we will use the curl standard program available on most platforms. In the following examples, we assume it has been correctly installed on your computer.

Launching NaviCell acting as a server

First, a identifier must be chosen to be used to communicate with the server. This identifier can be any sequence of letters, digits, underscores, hyphens or dots. If you are using a "official site" such as navicell.curie.fr, it is recommended that the identifier begins with your internet domain to avoid any session conflict.

For instance, let say that your domain is mydomain.net and your name is John Doe, then the chosen identifier may be net.mydomain.johndoe.
To launch the NaviCell server, type the following URL in your Web Browser (Google Chrome is recommended, but NaviCell also works with Firefox and Safari):

https://navicell.curie.fr/navicell/maps/cellcycle/master/index.php?id=@net.mydomain.johndoe

The CellCycle map will appear on your screen.

Controlling NaviCell server using the REST API

The communicate with the NaviCell server, we recommend to use a Shell variable containing the chosen identifier.

Open a Shell terminal and type the following command:
ID=the_chosen_identifier

For instance (but choose another one for your experiments):
ID=net.mydomain.johndoe

To increase the zoom level using the REST API, in the same terminal type the following command:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_set_zoom", "args": [10]}'

To decrease the zoom level:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_set_zoom", "args": [2]}'

To select the entities whose name match AKT1:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_find_entities", "args" : ["AKT1"]}'

To select the entities whose name start with A:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_find_entities", "args" : ["A*"]}'

Then to unselect all entities:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_uncheck_all_entities", "args" : []}'

To import and select a list of genes on map:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_import_datatables", "args": ["Gene list", "My GeneList", "", "@DATA\nGENE\nACOT13\nACR\nACTG1\n", {"import_display_markers": "checked"}]}'

Understanding the REST API

REST messages

A NaviCell REST message is under the form:
id=identifier&data=@COMMAND {"action": "command", "args" : [argument_list], "module" : "module_name"}'

where:

  1. id is the navicell server identifier
  2. action is the action to be executed
  3. args is a JSON array containing the arguments of the commands
  4. module is an optional argument containing the map or module name

The list of actions and their arguments are described in the section Reference Card.

Multiple commands

Several commands can be sent at the same time. For instance, to unselect all entities, select entities beginning with a B and setting the zoom level to 10:

curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=
@COMMAND {"action": "nv_uncheck_all_entities", "args" : []}
@COMMAND {"action": "nv_find_entities", "args" : ["B*"]}
@COMMAND {"action": "nv_set_zoom", "args": [10]}
'

Getting information from the server

The REST API can also be used to get information from the server. For instance, to get the HUGO names stored in the map:
curl 'https://navicell.curie.fr/cgi-bin/nv_proxy.php' -d 'id='$ID'&data=@COMMAND {"action": "nv_get_hugo_list", "args": []}'

A JSON dictionary is returned, with a status key and a data key. The HUGO names are stored in the data value:

{"status":0,"data":["ATM","ATR","CDK2","CHEK2","CREBBP","CCNA1","CCNA2", ...]}

Reference Card

This reference card describes all the actions and arguments currently provided by the NaviCell REST API.

Some examples are included in the tables. To make these examples work, do not forget to add id=the_chosen_identifier to the text displayed.

In the following examples, we assume that "MyExpression", "MyCopyNumber" and "MyMutation" are datatables that have been loaded and "OVARY_H123" is one of the samples contained in these datatables.

Navigation and Zooming

DescriptionAction NameArguments
Set map centernv_set_centerMAP_CENTER | MAP_EAST
MAP_SOUTH | MAP_NORTH
MAP_SOUTH_WEST | MAP_NORTH_EAST
MAP_SOUTH_EAST
 
--
Examplesdata=@COMMAND {"action": "nv_set_center", "args": ["MAP_CENTER"]}
data=@COMMAND {"action": "nv_set_center", "args": ["MAP_SOUTH_EAST"]}
Set map center (absolute position)nv_set_centerABSOLUTE posx :integerposy :integer
Exampledata=@COMMAND {"action": "nv_set_center", "args": ["ABSOLUTE", 100, 300]}
Move map centernv_set_centerRELATIVE posx :integerposy :integer
Exampledata=@COMMAND {"action": "nv_set_center", "args": ["RELATIVE", -10, -10]}
Set zoom levelnv_set_zoomzoom level :integer--
Exampledata=@COMMAND {"action": "nv_set_zoom", "args": [10]}

Entity Selection

DescriptionAction NameArguments
Select an entitynv_select_entityentity identifier :stringselect | toggle center :boolean
Exampledata=@COMMAND {"action": "nv_select_entity", "args": ["AKT1", "toggle", true]}
Find entitiesnv_find_entities_entityentity pattern :stringopen bubble :boolean-
Examplesdata=@COMMAND {"action": "nv_find_entities_entity", "args": ["AK*"]}
data=@COMMAND {"action": "nv_find_entities_entity", "args": ["AKT1", true]}
Uncheck all entitiesnv_uncheck_all_entities---
Exampledata=@COMMAND {"action": "nv_uncheck_all_entities", "args": []}
Unhighlight all entitiesnv_unhighlight_all_entities---
Exampledata=@COMMAND {"action": "nv_unhighlight_all_entities", "args": []}

Heatmap Editor

DescriptionAction NameCommand ArgumentArguments
Open heatmap editornv_heatmap_editor_performopen--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["open"]}
Close heatmap editornv_heatmap_editor_performclose--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["close"]}
Apply changesnv_heatmap_editor_performapply--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["apply"]}
Apply changes and closenv_heatmap_editor_performapply_and_close--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["apply_and_close"]}
Cancel changes and closenv_heatmap_editor_performcancel--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["cancel"]}
Select sample or groupnv_heatmap_editor_performselect_samplecolumn num :integersample name :string
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["select_sample", 1, "OVARY_H123"]}
Select datatablenv_heatmap_editor_performselect_datatablerow num :integerdatatable name :string
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["select_datatable", 1, "MyExpression"]}
Clear samplesnv_heatmap_editor_performclear_samples--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["clear_samples"]}
Select all samplesnv_heatmap_editor_performall_samples--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["all_samples"]}
Select all groupsnv_heatmap_editor_performall_groups--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["all_groups"]}
Import samples from barplotnv_heatmap_editor_performfrom_barplot--
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["from_barplot"]}
Set transparencynv_heatmap_editor_performset_transparencyvalue :integer [1:100]-
Exampledata=@COMMAND {"action": "nv_heatmap_editor_perform", "args": ["set_transparency", 90]}

Datatable Import

DescriptionAction NameArguments
Import a datatable from a URLnv_import_datatablesbiotype :biotypedatatable name :stringignored argument :stringURL :string
Exampledata=@COMMAND {"action": "nv_import_datatables", "args": ["Gene list", "MyGenes", "", "https://www.mydomain.net/my_genes.tsv"]}
Import a datatable from datanv_import_datatablesbiotype :biotypedatatable name :stringignored argument :stringdata :string beginning with @DATA\n
Exampledata=@COMMAND {"action": "nv_import_datatables", "args": ["Gene list", "MyGenes", "", "@DATA\nGENE\nABL1\nABR\nACACA\nACACB\nACAD9\nACHE\nACLY"]}

Sample Annotation Import

DescriptionAction NameCommand ArgumentArguments
Open sample annotation dialognv_sample_annotation_performopen--
Exampledata=@COMMAND {"action": "nv_sample_annotation_perform", "args": ["open"]}
Close sample annotation dialognv_sample_annotation_performclose--
Exampledata=@COMMAND {"action": "nv_sample_annotation_perform", "args": ["close"]}
Apply changesnv_sample_annotation_performapply--
Exampledata=@COMMAND {"action": "nv_sample_annotation_perform", "args": ["apply"]}
Cancel changes and closenv_sample_annotation_performcancel--
Exampledata=@COMMAND {"action": "nv_sample_annotation_perform", "args": ["cancel"]}
Import sample annotations from a URLnv_sample_annotation_performimportURL :string-
Exampledata=@COMMAND {"action": "nv_sample_annotation_perform", "args": ["import", "http://www.mydomain.net/my_sample_annotations.tsv"]}
Import sample annotations from datanv_sample_annotation_performimportdata :string beginning with @DATA\n-
Select/Unselect an annotationnv_sample_annotation_performselect_annotationannot name :stringchecked :boolean"Tissue", true :@example"Cancer Type", false :
Exampledata=@COMMAND {"action": "nv_sample_annotation_perform", "args": ["select_annotation", @example]}

MyData Dialog Management

DescriptionAction NameCommand Argument
Open MyData dialognv_mydata_performopen
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["open"]}
Close MyData dialognv_mydata_performclose
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["close"]}
Set "Datatables" tab activenv_mydata_performselect_datatables
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["select_datatables"]}
Set "Samples" tab activenv_mydata_performselect_samples
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["select_samples"]}
Set "Genes" tab activenv_mydata_performselect_genes
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["select_genes"]}
Set "Groups" tab activenv_mydata_performselect_groups
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["select_groups"]}
Set "Modules" tab activenv_mydata_performselect_modules
Exampledata=@COMMAND {"action": "nv_mydata_perform", "args": ["select_modules"]}

Drawing Configuration Dialog

DescriptionAction NameCommand ArgumentArguments
Open drawing configuration dialognv_drawing_config_performopen--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["open"]}
Close drawing configuration dialognv_drawing_config_performclose--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["close"]}
Apply changes drawing configuration dialognv_drawing_config_performapply--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["apply"]}
Apply changes and close drawing configuration dialognv_drawing_config_performapply_and_close--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["apply_and_close"]}
Cancel changes and close drawing configuration dialognv_drawing_config_performcancel--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["cancel"]}
Select heatmap displaynv_drawing_config_performselect_heatmapchecked :boolean-
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["select_heatmap", true]}
Select barplot displaynv_drawing_config_performselect_barplotchecked :boolean-
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["select_barplot", false]}
Select glyph displaynv_drawing_config_performselect_glyphglyph num :integerchecked :boolean
Examplesdata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["select_glyph", 1, true]}
data=@COMMAND {"action": "nv_drawing_config_perform", "args": ["select_glyph", 2, false]}
Select map staining displaynv_drawing_config_performselect_map_stainingchecked :boolean-
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["select_map_staining", true]}
Select "Display All Genes"nv_drawing_config_performdisplay_all_genes--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["display_all_genes"]}
Select "Display Selected Genes"nv_drawing_config_performdisplay_selected_genes--
Exampledata=@COMMAND {"action": "nv_drawing_config_perform", "args": ["display_selected_genes"]}

Barplot Editor

DescriptionAction NameCommand ArgumentArguments
Open barplot editornv_barplot_editor_performopen--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["open"]}
Close barplot editornv_barplot_editor_performclose--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["close"]}
Apply changesnv_barplot_editor_performapply--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["apply"]}
Apply changes and closenv_barplot_editor_performapply_and_close--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["apply_and_close"]}
Cancel changes and closenv_barplot_editor_performcancel--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["cancel"]}
Select sample or groupnv_barplot_editor_performselect_samplecolumn num :integersample name :string
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["select_sample", 2, "OVARY_H123"]}
Select datatablenv_barplot_editor_performselect_datatabledatatable name :string-
Clear samplesnv_barplot_editor_performclear_samples--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["clear_samples", "MyExpression"]}
Select all samplesnv_barplot_editor_performall_samples--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["all_samples"]}
Select all groupsnv_barplot_editor_performall_groups--
Exampledata=@COMMAND {"action": "nv_barplot_editor_perform", "args": ["all_groups"]}
Import samples from heatmapnv_barplot_editor_performfrom_heatmap--
Set transparencynv_barplot_editor_performset_transparencyvalue :integer [1:100]-

Glyph Editor

DescriptionAction NameCommand ArgumentArguments
Open glyph editornv_glyph_editor_performopenglyph num :integer-
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["open", 1]}
Close glyph editornv_glyph_editor_performcloseglyph num :integer-
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["close", 1]}
Apply changesnv_glyph_editor_performapplyglyph num :integer-
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["apply", 1]}
Apply changes and closenv_glyph_editor_performapply_and_closeglyph num :integer-
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["apply_and_close", 1]}
Cancel changes and closenv_glyph_editor_performcancelglyph num :integer-
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["cancel", 1]}
Select sample or groupnv_glyph_editor_performselect_sampleglyph num :integersample name :string
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["select_sample", 1, "OVARY_H123"]}
Select shape datatablenv_glyph_editor_performselect_datatable_shapeglyph num :integerdatatable name :string
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["select_datatable_shape", 1, "MyExpression"]}
Select color datatablenv_glyph_editor_performselect_datatable_colorglyph num :integerdatatable name :string
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["select_datatable_color", 1, "MyCopyNumber"]}
Select size datatablenv_glyph_editor_performselect_datatable_sizeglyph num :integerdatatable name :string
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["select_datatable_size", 1, "MyMutations"]}
Set transparencynv_glyph_editor_performset_transparencyglyph num :integervalue :integer [1:100]
Exampledata=@COMMAND {"action": "nv_glyph_editor_perform", "args": ["set_transparency", 1, 99]}

Map Staining Editor

DescriptionAction NameCommand ArgumentArguments
Open map staining editornv_map_staining_editor_performopen-
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["open"]}
Close map staining editornv_map_staining_editor_performclose-
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["close"]}
Apply changesnv_map_staining_editor_performapply-
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["apply"]}
Apply changes and closenv_map_staining_editor_performapply_and_close-
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["apply_and_close"]}
Cancel changes and closenv_map_staining_editor_performcancel-
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["cancel"]}
Select sample or groupnv_map_staining_editor_performselect_samplesample name :string
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["select_sample", "OVARY_H123"]}
Select datatablenv_map_staining_editor_performselect_datatabledatatable name :string
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["select_datatable", "MyExpression"]}
Set transparencynv_map_staining_editor_performset_transparencyvalue :integer [1:100]
Exampledata=@COMMAND {"action": "nv_map_staining_editor_perform", "args": ["set_transparency", 90]}

Display Continuous Configuration Editor

DescriptionAction NameCommand ArgumentArguments
Open editornv_display_continuous_config_performopendatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["open", "MyExpression", "shape"]}
Close editornv_display_continuous_config_performclosedatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["close", "MyExpression", "size"]}
Apply changesnv_display_continuous_config_performapplydatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["apply", "MyExpression", "color"]}
Apply changes and closenv_display_continuous_config_performapply_and_closedatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["apply_and_close", "MyExpression", "shape"]}
Cancel changes and closenv_display_continuous_config_performcanceldatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["cancel", "MyExpression", "color"]}
Set step countnv_display_continuous_config_performstep_count_changesample|group shape|size|color datatable name :stringstep count :integer-
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["step_count_change", ""sample", "color", "MyExpression", 4]}
Set absolute value modenv_display_continuous_config_performset_sample_absvalshape|size|color datatable name :stringchecked :boolean--
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_sample_absval", "size", "MyExpression", true]}
Set sample methodnv_display_continuous_config_performset_sample_methodshape|size|color datatable name :stringmethod :string--
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_sample_method", "size", "MyExpression", 3]}
Set group methodnv_display_continuous_config_performset_group_methodshape|size|color datatable name :stringmethod :string--
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_group_method", "size", "MyExpression", 3]}
Set input valuenv_display_continuous_config_performset_input_valuedatatable name :stringshape|size|color sample|group index :integervalue :double
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_input_value", "size", "sample", 2, 12.345]}
Set selection colornv_display_continuous_config_performset_input_colordatatable name :stringcolor sample|group index :stringcolor :integer
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_input_color", "color, "group", 3, "FFFFFF"]}
Set selection sizenv_display_continuous_config_performset_select_sizedatatable name :stringsize sample|group index :integersize :integer
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_select_size", "size", "sample", 2, 8]}
Set selection shapenv_display_continuous_config_performset_select_shapedatatable name :stringshape sample|group index :integershape :integer
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["set_select_shape", "shape", "sample", 4]}
Switch to "Sample" tabnv_display_continuous_config_performswitch_sample_tabdatatable name :stringshape|size|color ---
Examplesdata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["switch_sample_tab", "MyExpression", "shape"]}
data=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["switch_sample_tab", "MyCopyNumber", "size"]}
Switch to "Group" tabnv_display_continuous_config_performswitch_sample_groupdatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_continuous_config_perform", "args": ["switch_sample_group", "MyExpression", "color"]}

Display Unordered Discrete Configuration Editor

DescriptionAction NameCommand ArgumentArguments
Open editornv_display__unordered_discrete_config_performopendatatable name :stringshape|size|color ---
Examplesdata=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["open", "MyMutation", "shape"]}
data=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["open", "MyMutation", "size"]}
Close editornv_display__unordered_discrete_config_performclosedatatable name :stringshape|size|color ---
Examplesdata=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["close", "MyMutation", "shape"]}
data=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["close", "MyMutation", "size"]}
Apply changesnv_display__unordered_discrete_config_performapplydatatable name :stringshape|size|color ---
Examplesdata=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["apply", "MyMutation", "color"]}
data=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["apply", "MyMutation", "size"]}
Apply changes and closenv_display__unordered_discrete_config_performapply_and_closedatatable name :stringshape|size|color ---
Examplesdata=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["apply_and_close", "MyMutation", "color"]}
data=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["apply_and_close", "MyMutation", "size"]}
Cancel changes and closenv_display__unordered_discrete_config_performcanceldatatable name :stringshape|size|color ---
Examplesdata=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["cancel", "MyMutation", "color"]}
data=@COMMAND {"action": "nv_display__unordered_discrete_config_perform", "args": ["cancel", "MyMutation", "size"]}
Open/Close advanced configurationnv_display_unordered_discrete_config_performset_advanced_configurationdatatable name :stringshape|size|color checked :boolean--
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["set_advanced_configuration", "MyMutation", "shape", "color", true]}
Set discrete valuenv_display_unordered_discrete_config_performset_discrete_valuedatatable name :stringshape|size|color sample|group index :integervalue :double
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["set_discrete_value", "MyMutation", "shape", "sample", 2, 4]}
Set discrete colornv_display_unordered_discrete_config_performset_discrete_colordatatable name :stringcolor sample|group index :stringcolor :integer
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["set_discrete_color", "MyMutation", "color", "sample", 3, "FF0000"]}
Set discrete sizenv_display_unordered_discrete_config_performset_discrete_sizedatatable name :stringsize sample|group index :integersize :integer
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["set_discrete_size", "MyMutation", "sample", 3, 10]}
Set discrete shapenv_display_unordered_discrete_config_performset_discrete_shapedatatable name :stringshape sample|group index :integershape :integer
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["set_discrete_shape", "MyMutation", "shape", "sample", 2, 5]}
Set discrete conditionnv_display_unordered_discrete_config_performset_discrete_conddatatable name :stringshape|size|color sample|group index :integercondition :integer
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["set_discrete_cond", "MyMutation", "shape", "sample", 3, 2]}
Switch to "Sample" tabnv_display_unordered_discrete_config_performswitch_sample_tabdatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["switch_sample_tab", "MyMutation", "size"]}
Switch to "Group" tabnv_display_unordered_discrete_config_performswitch_sample_groupdatatable name :stringshape|size|color ---
Exampledata=@COMMAND {"action": "nv_display_unordered_discrete_config_perform", "args": ["switch_sample_group", "MyMutation", "shape"]}

Message Display

DescriptionAction NameCommand ArgumentArguments
Open message windownv_notice_performopen-----
Exampledata=@COMMAND {"action": "nv_notice_perform", "args": ["open"]}
Close message windownv_notice_performclose-----
Exampledata=@COMMAND {"action": "nv_notice_perform", "args": ["close"]}
Open message window and display a messagenv_notice_performset_message_and_openheader :stringmessage :stringposition :stringwidth :integerheight :integer
Exampledata=@COMMAND {"action": "nv_notice_perform", "args": ["set_message_and_open", "Notice", "Type AK* in the search form and type returns", "top-left", 200, 200]}

Getting Information from the Server

DescriptionAction Name
Get HUGO list in mapnv_get_hugo_list
Exampledata=@COMMAND {"action": "nv_get_hugo_list", "args": []}
Get module listnv_get_module_list
Exampledata=@COMMAND {"action": "nv_get_module_list", "args": []}
Get imported datatablesnv_get_datatable_list
Exampledata=@COMMAND {"action": "nv_get_datatable_list", "args": []}
Get genes in imported datatablesnv_get_datatable_gene_list
Exampledata=@COMMAND {"action": "nv_get_datatable_gene_list", "args": []}
Get samples in imported datatablesnv_get_datatable_sample_list
Exampledata=@COMMAND {"action": "nv_get_datatable_sample_list", "args": []}
Get biotype list in NaviCellnv_get_biotype_list
Exampledata=@COMMAND {"action": "nv_get_biotype_list", "args": []}
Get command historynv_get_command_history
Exampledata=@COMMAND {"action": "nv_get_command_history", "args": []}

Client/Server Synchronisation

DescriptionAction Name
Returns true when server is readynv_is_ready
Exampledata=@COMMAND {"action": "nv_is_ready", "args": []}
Returns true when datatable or sample are importednv_is_imported
Exampledata=@COMMAND {"action": "nv_is_imported", "args": []}