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Omics Visualizer Automation Documentation

Omics Visualizer version 1.3.0

Last update: 2020-03-31

List of commands

Manage tables

Visualizations

Legends

Access GUI dialogs

Connect

ov connect

Connect the current table with the current network

Arguments

  • mappingColNet (required) String

    Key column from the Network node table used to map the network with the table. The column should be a shared column.

  • mappingColTable (required) String

    Key column from the Omics Visualizer table used to map the table with the network.

Example

ov connect mappingColNet="gene name" mappingColTable="name"

This will link the active OV table with the current network. The OV table must have a column named name and the node table from the network must have a column named gene name. Those two columns are used to link the two tables.

List of commands - List of Manage tables commands

Connect show

ov connect show

Show the connect window of the current table

List of commands - List of Access GUI dialogs commands

Disconnect

ov disconnect

Disconnect the current table and the current network if they are already connected

List of commands - List of Manage tables commands

Filter

ov filter

Filters the row of an Omics Visualizer table

Arguments

  • filter (required) String

    The filter is defined by the following non-contextual grammar:
    filter = and | or | criteria
    and = {filter_list}
    or = [filter_list]
    filter_list = filter,filter_list | filter
    criteria = (colName,operator,value)

    where 'colName' is the name of the column (commas in colName should be escaped by being preceeded a backslash)
    'operator' is the name of the operation applied, the list of operators is available with the command ov filter list operators
    'value' if necessary, is the value to compare with. Careful with the regex and escaped characters.

  • tableName (optional) String

    OV table name.
    By default the active table is used, if you want to use another one you can specify its name here.

Example

ov filter filter="{(p-value,LOWER_EQUALS,0.05),[(ontology,CONTAINS,GO),(ontology,NULL,)]}"

This will select the rows where the p-value is lower or equals to 0.05 and the ontology is either from the Gene Ontology (contains "GO") or unknown (the value is null).

List of commands - List of Manage tables commands

Filter list operators

ov filter list operators

List the available operators

The list of current available operators is:

  • EQUALS (String, boolean, numbers) the table value should match exactly the reference value
  • NOT_EQUALS (String, boolean, numbers) the table value should not match the reference value
  • CONTAINS (String) a part of the table value should match exactly the reference value
  • NOT_CONTAIN (String) a part of the table value should match exactly the reference value
  • MATCHES (String) the table value should match exactly the regular expression from the reference value
  • LOWER (numbers) the table value should be strictly lower than the reference value
  • LOWER_EQUALS (numbers) the table value should be lower than or equals to the reference value
  • GREATER (numbers) the table value should be strictly greater than the reference value
  • GREATER_EQUALS (numbers) the table value should be greater than or equals to the reference value
  • NULL (String, boolean, numbers) the table value should be null
  • NOT_NULL (String, boolean, numbers) the table value should not be null

List of commands

Filter remove

ov filter remove

Removes the filter of the active table

List of commands - List of Manage tables commands

Filter show

ov filter show

Show the filter window of the current table

List of commands - List of Access GUI dialogs commands

Import node table

ov import node table

Transform node table into an Omics Visualizer table

Arguments

  • importedColNames (optional) String

    Comma-separated list of column names to import into the new Omics Visualizer table. Commas in the column names should be escaped.

  • importedNamespaces (optional) String

    Comma-separated list of column namespaces to import into the new Omics Visualizer table. All the columns from those namespaces will be imported. Commas in the column namespaces should be escaped.

  • keyColName (required) String

    Name of the shared column that identifies the row in the node table.

  • newTableName (optional) String

    The name of the new Omics Visualizer table. A default generated name will be given if omitted.

  • srcName (optional) String Default: source, or the namespace if all the selected columns are from the same namespace.

    The name of the column containing the values source.

  • srcNetwork (required) CyNetwork

    The network containing the node table.

  • valuesName (optional) String Default: value

    The name of the column containing the values.

Nota Bene: importedColNames and importedNamespaces are optional, but at least one of them should be filled.

Example

ov import node table srcNetwork="String Network" keyColName="display name" importedNamespaces="tissue" srcName="tissue" newTableName="String tissues"

This will import the columns from the "tissue" namespace of "String Network". The new Omics Visualizer table named "String tissues" will be connected with "String Network" with the column "display name". The column of "String tissues" that contains the name of the node table column is named "tissue".

List of commands - List of Manage tables commands

Legend draw

ov legend draw

Draw a legend

Arguments

  • fitView (optional) boolean Default: true

    Should the view of the network be fitted to the content after the legend is added.

  • fontName (optional) String Default: "SansSerif"

    The font family.

  • fontSize (optional) int Default: 22

    The font size.

  • includeInner (optional) boolean Default: true if there is an inner visualization, false otherwise

    Should the inner visualization included in the legend?

  • includeOuter (optional) boolean Default: true if there is an outer visualization, false otherwise

    Should the outer visualization included in the legend?

  • orientation (optional) String Default: "HORIZONTAL"

    The orientation of the legend.
    Must be one of:

    • "HORIZONTAL"
    • "VERTICAL"

  • position (optional) String Default: "NORHT_LEFT"

    The position of the legend.
    Must be one of:

    • "NORTH" the legend will be on top of the network, centered
    • "NORTH_LEFT" the legend will be on top of the network, aligned left
    • "NORTH_RIGHT" the legend will be on top of the network, aligned right
    • "SOUTH" the legend will be at the bottom of the network, centered
    • "SOUTH_LEFT" the legend will be at the bottom of the network, aligned left
    • "SOUTH_RIGHT" the legend will be at the bottom of the network, aligned right
    • "EAST" the legend will be on the right of the network, aligned with the middle
    • "EAST_TOP" the legend will be on the right of the network, aligned top
    • "EAST_BOTTOM" the legend will be on the right of the network, aligned bottom
    • "WEST" the legend will be on the left of the network, aligned with the middle
    • "WEST_TOP" the legend will be on the left of the network, aligned top
    • "WEST_BOTTOM" the legend will be on the left of the network, aligned bottom

  • showTitle (optional) boolean Default: false

    Should the title be added to the legend?

  • title (optional) String Default: the network name

    The title of the legend.
    If you don't want any title, you give an empty title.

Example

ov legend draw orientation="VERTICAL" position="EAST_TOP" title=""

This will generate a legend containing all the visualizations (inner and/or outer, if any) with no title. The legend will be drawned vertically at the right of the network, aligned with the top of it.

List of commands - List of Legends commands

Legend hide

ov legend hide

Hide a legend

List of commands - List of Legends commands

Load

ov load

Load an Omics Visualizer table.
Returns the name of the newly imported OV table.

Arguments

  • dataTypeList (optional) String

    List of column data types ordered by column index (e.g. "string,int,long,double,boolean,intlist" or just "s,i,l,d,b,il").
    If not given, the types will be automatically detected.

  • decimalSeparator (optional) Character Default: '.'

    Character that separates the integer-part (characteristic) and the fractional-part (mantissa) of a decimal number.

  • delimiters (optional) String Default: "," if CSV, TAB otherwise

    Select the delimiters to use to separate columns in the table.
    Must be one of:

    • ","
    • " "
    • "\t"
    • ";"

  • delimitersForDataList (optional) Character Default: '|'

    The delimiters between elements of list columns in the table.
    Must be one of:

    • '|'
    • '\'
    • '/'
    • ','

  • file (required) String

    The path to the file that contains the table or network to be imported.

  • firstRowAsColumnNames (optional) boolean Default: true

    Does the first imported row contains column names?

  • newTableName (optional) String

    The title of the new table.
    If no title is given, then a name will be generated, started by "Omics Visualizer Table" followed by a number.

  • startLoadRow (optional) int Default: 1

    The first row of the input table to load. This allows the skipping of headers that are not part of the import.

Example

ov load file="/path/to/myfile.csv" newTableName="myData"

This loads the file "myfile.csv" into Omics Visualizer and create the corresponding table with the name "myData".

List of commands - List of Manage tables commands

Palette list

ov palette list

List available palettes with their provider

List of commands

Retrieve

ov retrieve

Retrieve a STRING network and connects it to the active OV table.

Arguments

  • cutoff (optional) Double Default: 0.4

    Confidence (score) cutoff. Must be between 0.0 and 1.0.

  • filteredOnly (optional) boolean Default: true

    Only filtered rows should be used to the query?

  • queryColumn (required) String

    Column name of the Omics Visualizer Table.

  • selectedOnly (optional) boolean Default: false

    Only selected rows should be used to the query ?

  • species (optional) String

    Name of the species to query.

  • taxonID (optional) int

    Identifier of the species to query.

Nota Bene: species and taxonID are optional, but at least one of them should be filled.

Example

ov retrieve queryColumn="UniProt" taxonID=9606

This retrieves a STRING network for the active OV table. The query is made on UniProt values from the OV table for Human (taxon 9606).

List of commands - List of Manage tables commands

Retrieve show

ov retrieve show

Show the retrieve window of the current table

List of commands - List of Access GUI dialogs commands

Table delete

ov table delete

Delete the active Omics Visualizer table

List of commands - List of Manage tables commands

Table list

ov table list

Get the list of Omics Visualizer tables

List of commands - List of Manage tables commands

Table set current

ov table set current

Set the current Omics Visualizer table

Argument

  • tableName (required) String

    Name of the OV table to set as active

Example

ov table set current tableName="myData"

This sets the OV table named "myData" as the active one.

List of commands - List of Manage tables commands

Version

ov version

Returns the current version of the app

List of commands

Viz apply inner continuous

ov viz apply inner continuous

Apply an inner visualization (pie charts) with a continuous mapping

Arguments

  • attributes (required) String

    Name of the column that contains the data you want to visualize.

  • chartSettings (optional) String

    Comma separated list of enhancedGraphics settings.
    Here is how the string should be formatted: "setting1:value1,setting2:value2" e.g. "arcstart:0,arcdirection:counterclockwise"

  • colorMax (optional) String

    Color used in the gradient as the highest value.

  • colorMid (optional) String

    Color used in the gradient as the middle value.

  • colorMin (optional) String

    Color used in the gradient as the lowest value.

  • colorMissing (optional) String

    Color used for missing values.

  • filteredOnly (optional) boolean Default: true

    Use all the data (false) or only the filtered one (true)?

  • labels (optional) String

    Column name of the table that should be used to label the data. By default no label is displayed.

  • paletteName (optional) String

    Name of the palette to use as default colors. (See ov palette list)

  • paletteProviderName (optional) String

    Name of the palette provider of the palette. (See ov palette list)

  • rangeMax (optional) double

    Maximum value. Above this value, the same color will be applied.

  • rangeMid (optional) double

    Middle value. The colors will be a gradient from min to mid, and from mid to max.

  • rangeMin (optional) double

    Minimum value. Below this value, the same color will be applied.

Examples

ov viz apply inner continuous attributes="log ratio" rangeMin=-5 rangeMax=5

This will create a pie chart visualization from the "log ratio" column, using the default palette colors with a range from -5 to 5.

ov viz apply inner continuous attributes="log ratio" rangeMin=-5 rangeMax=5 paletteName="Purple-Orange" paletteProviderName="ColorBrewer"

This will create a pie chart visualization from the "log ratio" column, using the specified palette colors with a range from -5 to 5.

ov viz apply inner continuous attributes="log ratio" rangeMin=-5 rangeMax=5 colorMin="blue" colorMid="white" colorMax="red"

This will create a pie chart visualization from the "log ratio" column, using the specified colors with a range from -5 to 5.

List of commands - List of Visualizations commands

Viz apply inner discrete

ov viz apply inner discrete

Apply an inner visualization (pie charts) with a discrete mapping

Arguments

  • attributes (required) String

    Name of the column that contains the data you want to visualize.

  • chartSettings (optional) String

    Comma separated list of enhancedGraphics settings.
    Here is how the string should be formatted: "setting1:value1,setting2:value2" e.g. "arcstart:0,arcdirection:counterclockwise"

  • colorMapping (optional) String

    Comma separated values of mappings value:color. Special characters in values must be escaped.

  • colorMissing (optional) String

    Color used for missing values.

  • filteredOnly (optional) boolean Default: true

    Use all the data (false) or only the filtered one (true)?

  • labels (optional) String

    Column name of the table that should be used to label the data. By default no label is displayed.

  • paletteName (optional) String

    Name of the palette to use as default colors. (See ov palette list)

  • paletteProviderName (optional) String

    Name of the palette provider of the palette. (See ov palette list)

Example

ov viz apply inner discrete attributes="cluster" colorMapping="A:blue,B:orange,C:red"

This will create a pie chart visualization with the "cluster" column. The value "A" will be blue, "B" orange and "C" red. If there are more values in the "cluster" column, a default color from the default palette will be assigned.

List of commands - List of Visualizations commands

Viz apply outer continuous

ov viz apply outer continuous

Apply an outer visualization (donuts charts) with a continuous mapping

Arguments

  • attributes (required) String

    Comma separated value list of attributes from the table you want to visualize the data. Special characters in the attributes must be escaped.

  • chartSettings (optional) String

    Comma separated list of enhancedGraphics settings.
    Here is how the string should be formatted: "setting1:value1,setting2:value2" e.g. "arcstart:0,arcdirection:counterclockwise"

  • colorMax (optional) String

    Color used in the gradient as the highest value.

  • colorMid (optional) String

    Color used in the gradient as the middle value.

  • colorMin (optional) String

    Color used in the gradient as the lowest value.

  • colorMissing (optional) String

    Color used for missing values.

  • filteredOnly (optional) boolean Default: true

    Use all the data (false) or only the filtered one (true)?

  • labels (optional) String

    Column name of the table that should be used to label the data. By default no label is displayed.

  • paletteName (optional) String

    Name of the palette to use as default colors. (See ov palette list)

  • paletteProviderName (optional) String

    Name of the palette provider of the palette. (See ov palette list)

  • rangeMax (optional) double

    Maximum value. Above this value, the same color will be applied.

  • rangeMid (optional) double

    Middle value. The colors will be a gradient from min to mid, and from mid to max.

  • rangeMin (optional) double

    Minimum value. Below this value, the same color will be applied.

  • transpose (optional) boolean Default: false

    Should the ring represents a column (false) or a row (true)?

Example

ov viz apply outer continuous attributes="log1,log2,log3" rangeMin=-2 rangeMax=2

This will create a donut chart visualization with three rings: "log1", "log2", and "log3". The colors are automatically assigned according to the default palette with a range from -2 to 2.

List of commands - List of Visualizations commands

Viz apply outer discrete

ov viz apply outer discrete

Apply an outer visualization (donuts charts) with a discrete mapping

Arguments

  • attributes (required) String

    Comma separated value list of attributes from the table you want to visualize the data. Special characters in the attributes must be escaped.

  • chartSettings (optional) String

    Comma separated list of enhancedGraphics settings.
    Here is how the string should be formatted: "setting1:value1,setting2:value2" e.g. "arcstart:0,arcdirection:counterclockwise"

  • colorMapping (optional) String

    Comma separated values of mappings value:color. Special characters in values must be escaped.

  • colorMissing (optional) String

    Color used for missing values.

  • filteredOnly (optional) boolean Default: true

    Use all the data (false) or only the filtered one (true)?

  • labels (optional) String

    Column name of the table that should be used to label the data. By default no label is displayed.

  • paletteName (optional) String

    Name of the palette to use as default colors. (See ov palette list)

  • paletteProviderName (optional) String

    Name of the palette provider of the palette. (See ov palette list)

  • transpose (optional) boolean Default: false

    Should the ring represents a column (false) or a row (true)?

Example

ov viz apply outer discrete attributes="cluster1,cluster2"

This will create a donut chart visualization with two rings: the "cluster1" and "cluster2" values. The colors for each value will be automatically generated using the default palette.

List of commands - List of Visualizations commands

Viz remove inner

ov viz remove inner

Remove the inner Visualization (pie charts) of the current network

List of commands - List of Visualizations commands

Viz remove outer

ov viz remove outer

Remove the outer Visualization (donuts charts) of the current network

List of commands - List of Visualizations commands

Viz show inner

ov viz show inner

Show the inner visualization (pie charts) window of the current table

List of commands - List of Access GUI dialogs commands

Viz show outer

ov viz show outer

Show the outer visualization (donuts charts) window of the current table

List of commands - List of Access GUI dialogs commands