Automating EnrichmentMap

EnrichmentMap provides several commands which allow basic features to be automated via scripts, the command line or REST.

Note

For more details on the Command Line Dialog and Cytoscape command syntax see the Cytoscape User Docs

Note

For more details on using CyRest to call commands via REST see the CyREST Documentation

List of Available Commands

The provided commands are in the enrichmentmap namespace.

Command
Description
enrichmentmap build
Creates an EnrichmentMap network containing one or two
data sets.
enrichmentmap mastermap
Creates an EnrichmentMap network containing any
number of data sets by scanning files in a folder.
enrichmentmap mastermap list
Scans files in a folder and prints out how they would
be grouped into data sets, but does not create a network.
This command is intended to help debug the
‘mastermap’ command by showing how the files will be
grouped into data sets without actually creating the network.
enrichmentmap build-table
Creates an EnrichmentMap network from values in a table.
enrichmentmap pa
Runs post-analysis. Adds more gene sets to an existing
network. This is done by calculating the overlap between
gene sets of the current EnrichmentMap network and all the
gene sets contained in the provided signature gene set file.
enrichmentmap chart
Sets the chart options for an EnrichmentMap network.
enrichmentmap dataset hide
Allows to de-select the data sets to show in an
EnrichmentMap network.
enrichmentmap dataset show
Allows to select the data sets to show in an EnrichmentMap
network.
enrichmentmap export model
Exports the EnrichmentMap data model to a file. Intended
mainly for debugging.
enrichmentmap export pdf
Exports the contents of the Heat Map panel to a PDF file.
enrichmentmap gseabuild
Creates an EnrichmetMap network from one or two GSEA
results.
(Deprecated, use ‘build’ or ‘mastermap’ command instead.)

Commands

enrichmentmap build

Creates an EnrichmentMap network containing one or two data sets.

Arguments:

analysisType (GSEA|generic|DAVID/BiNGO/Great)

Analysis Type

classDataset1 <File path>

Path to Classes File for Dataset 1 specifying the classes of each sample in expression file. Format: see GSEA website

classDataset2 <File path>

Path to Classes File for Dataset 2 specifying the classes of each sample in expression file. format: see GSEA website

coefficients (OVERLAP|JACCARD|COMBINED)

Used to choose the formula used to calculate the similarity score.

coeffecients (OVERLAP|JACCARD|COMBINED)

Deprecated, use ‘coefficients’ instead.

combinedConstant <double>

When coefficients=COMBINED this parameter is used to determine what percentage to use for JACCARD and OVERLAP when combining their value.Value between 0 and 1, where 0 means 100% JACCARD and 0% OVERLAP, and 1 means 0% JACCARD and 100% OVERLAP.

edgeStrategy (AUTOMATIC|DISTINCT|COMPOUND)

DISTINCT: Create separate edges for each data set when appropriate. A separate similarity score will be calculated for each data set. COMPOUND: Gene sets with the same name are combined (set union) and then the similarity score is calculated. AUTOMATIC: EnrichmentMap decides which of the previous options to use. See the EnrichmentMap documentation for more details.

enrichments2Dataset1 <File path>

Path to a second Enrichments File for Dataset 1 specifying enrichment results.

enrichments2Dataset2 <File path>

Path to a second Enrichments File for Dataset 2 specifying enrichment results.

enrichmentsDataset1 <File path>

Path to Enrichments File for Dataset 1 specifying enrichment results.

enrichmentsDataset2 <File path>

Path to Enrichments File for Dataset 2 specifying enrichment results.

expressionDataset1 <File path>

Path to Expression File for Dataset 1 with gene expression values. Format: gene description expression value …

expressionDataset2 <File path>

Path to Expression File for Dataset 2 with gene expression values. Format: gene description expression value …

filterByExpressions true|false

If true then genes that are contained in the gene set (GMT) files or the enrichment files, but are not contained in the expression files will not be included in the network.

gmtFile <File path>

Path to GMT File specifying gene sets. Format: geneset name description gene …

pvalue <Double>

P-value Cutoff (value between 0 and 1). Gene set nodes with a p-value lower than the given value will not be included in the network.

qvalue <Double>

FDR Q-value Cutoff (value between 0 and 1). Gene set nodes with a q-value lower than the one entered will not be included in the network.

ranksDataset1 <File path>

Path to a Ranks File for Dataset 1 specifying ranked genes. Format: gene score or statistic

ranksDataset2 <File path>

Path to Ranks File for Dataset 2 specifying ranked genes. Format: gene score or statistic

similaritycutoff <Double>

Similarity Cutoff (value between 0 and 1). Edges with a similarity score lower than the one entered will not be included in the network.

minExperiments <Integer>

A gene set must be included in this many data sets to be included in the network (optional).

nesFilter (ALL|POSITIVE|NEGATIVE)

POSITIVE: Only gene sets from the positive enrichment file will be included. NEGATIVE: Only gene sets from the negative enrichment file will be included. All: Both enrichment files will be included

networkName <String>

The name of the EnrichmentMap network. If not provided then EnrichmentMap will automatically generate a name for the network based on the name of the first data set.

phenotype1Dataset1 <String>

Phenotype 1 for Dataset 1

phenotype1Dataset2 <String>

Phenotype 1 for Dataset 2

phenotype2Dataset1 <String>

Phenotype 2 for Dataset 1

phenotype2Dataset2 <String>

Phenotype 2 for Dataset 2

enrichmentmap mastermap

Creates an EnrichmentMap network containing any number of data sets by scanning files in a folder. Uses the same algorithm as the Create EnrichmentMap Dialog to scan the files in a folder and automatically group them into data sets. Sub-folders will be scanned up to one level deep, allowing you to organize your data sets into sub-folders under the root folder. See Scanning Heuristic.

Arguments:

rootFolder <file path>

Absolute path to a folder containing the data files. The files will be scanned and automatically grouped into data sets. Sub-folders will be scanned up to one level deep.

pattern <string>

A glob-style path filter. Sub-folders inside the root folder that do not match the pattern will be ignored. For more details on syntax see docs for Java glob syntax

pvalue <double>

P-value Cutoff (value between 0 and 1). Gene set nodes with a p-value lower than the given value will not be included in the network.

qvalue <double>

FDR Q-value Cutoff (value between 0 and 1). Gene set nodes with a q-value lower than the one entered will not be included in the network.

similaritycutoff <double>

Similarity Cutoff (value between 0 and 1). Edges with a similarity score lower than the one entered will not be included in the network.

coefficients (OVERLAP|JACCARD|COMBINED)

Used to choose the formula used to calculate the similarity score. Default is OVERLAP.

combinedConstant <double>

When coefficients=COMBINED this parameter is used to determine what percentage to use for JACCARD and OVERLAP when combining their value. Value between 0 and 1, where 0 means 100% JACCARD and 0% OVERLAP, and 1 means 0% JACCARD and 100% OVERLAP.

commonExpressionFile <file path>

Absolute path to an expression file that will be used for every data set. Overrides other expression files.

commonGMTFile <file path>

Absolute path to a GMT file that will be used for every data set. Overrides other GMT files.

edgeStrategy (AUTOMATIC|DISTINCT|COMPOUND)

DISTINCT: Create separate edges for each data set when appropriate. A separate similarity score will be calculated for each data set. COMPOUND: Gene sets with the same name are combined (set union) and then the similarity score is calculated. AUTOMATIC: EnrichmentMap decides which of the previous options to use. Default is AUTOMATIC.

filterByExpressions true|false

If true then genes that are contained in the gene set (GMT) files or the enrichment files, but are not contained in the expression files will not be included in the network.

minExperiments <integer>

A gene set must be included in this many data sets to be included in the network (optional).

nesFilter (ALL|POSITIVE|NEGATIVE)

POSITIVE: Only gene sets from the positive enrichment file will be included. NEGATIVE: Only gene sets from the negative enrichment file will be included. All: Both enrichment files will be included. Default is ALL.

networkName <string>

The name of the EnrichmentMap network. If not provided then EnrichmentMap will automatically generate a name for the network based on the name of the first data set.

enrichmentmap mastermap list

Scans files in a folder and prints out how they would be grouped into data sets, but does not create a network. This command is intended to help debug the ‘mastermap’ command by showing how the files will be grouped into data sets without actually creating the network. See Scanning Heuristic.

Arguments:

rootFolder <file path>

Absolute path to a folder containing the data files. The files will be scanned and automatically grouped into data sets. Sub-folders will be scanned up to one level deep.

pattern <string>

A glob-style path filter. Sub-folders inside the root folder that do not match the pattern will be ignored. For more details on syntax see docs for Java glob syntax

enrichmentmap build-table

Creates an EnrichmentMap network from values in a table. Intended mainly for other Apps to programatically create an EnrichmentMap network.

Arguments:

table <String>

Name of the table to import from. If the prefix `SUID:` is used, the table corresponding the SUID will be returned. Example: “galFiltered.sif default node”

genesColumn <String>

Name of column that contains the list of genes.

nameColumn <String>

Name of column that contains the names of the gene sets.

pvalueColumn <String>

Name of column that contains p values.

descriptionColumn <String>

Name of column that contains the gene set description (optional).

coefficients (OVERLAP|JACCARD|COMBINED)

Used to choose the formula used to calculate the similarity score.

combinedConstant <double>

When coefficients=COMBINED this parameter is used to determine what percentage to use for JACCARD and OVERLAP when combining their value.Value between 0 and 1, where 0 means 100% JACCARD and 0% OVERLAP, and 1 means 0% JACCARD and 100% OVERLAP.

edgeStrategy (AUTOMATIC|DISTINCT|COMPOUND)

DISTINCT: Create separate edges for each data set when appropriate. A separate similarity score will be calculated for each data set. COMPOUND: Gene sets with the same name are combined (set union) and then the similarity score is calculated. AUTOMATIC: EnrichmentMap decides which of the previous options to use. See the EnrichmentMap documentation for more details.

filterByExpressions true|false

If true then genes that are contained in the gene set (GMT) files or the enrichment files, but are not contained in the expression files will not be included in the network.

minExperiments <Integer>

A gene set must be included in this many data sets to be included in the network (optional).

nesFilter (ALL|POSITIVE|NEGATIVE)

POSITIVE: Only gene sets from the positive enrichment file will be included. NEGATIVE: Only gene sets from the negative enrichment file will be included. All: Both enrichment files will be included

pvalue <Double>

P-value Cutoff (value between 0 and 1). Gene set nodes with a p-value lower than the given value will not be included in the network.

qvalue <Double>

FDR Q-value Cutoff (value between 0 and 1). Gene set nodes with a q-value lower than the one entered will not be included in the network.

similaritycutoff <Double>

Similarity Cutoff (value between 0 and 1). Edges with a similarity score lower than the one entered will not be included in the network.

networkName <String>

The name of the EnrichmentMap network. If not provided then EnrichmentMap will automatically generate a name for the network based on the name of the first data set.

enrichmentmap pa

Runs post-analysis. Adds more gene sets to an existing network. This is done by calculating the overlap between gene sets of the current EnrichmentMap network and all the gene sets contained in the provided signature gene set file.

Arguments:

network current|[column:value|network name]:

The EnrichmentMap network.

dataSetName <String>

Name of existing data set to run PA against, or “ALL” to run in batch mode against all data sets.

cutoff <double>

Edges with a similarity score lower than the one entered will not be included in the network.

filterType (NO_FILTER|HYPERGEOM|MANN_WHIT_TWO_SIDED|MANN_WHIT_GREATER| MANN_WHIT_LESS|NUMBER|PERCENT|SPECIFIC)

Type of statistical test to use for edge weight. Please see the EnrichmentMap documentation for more details.

gmtFile <File path>

Absolute path to GMT file containing gene sets to add to the network.

hypergeomUniverseType (GMT|EXPRESSION_SET|INTERSECTION|USER_DEFINED)

When ‘filterType’ is HYPERGEOM allows to choose how the value for N is calculated.

userDefinedUniverseSize <int>

When ‘hypergeomUniverseType’ is USER_DEFINED, sets the value for N.

mannWhitRanks <MannWhitRanks>

When using Mann-Whitney allows to specify which rank file to use with each dataset. Example usage “DataSetName1:RankFile1,DataSetName2:RankFile2”

name <String>

Name of the signature data set that will be created.

enrichmentmap chart

Sets the chart options for an EnrichmentMap network. This command is basically the same as setting the chart options in the main EnrichmentMap panel.

Arguments:

colors (RD_BU_9|RD_BU_3|BR_BG_3|PI_YG_3|PU_OR_3|RD_YL_BU_3)

Sets the chart colors.

data (NES_VALUE|P_VALUE|FDR_VALUE|PHENOTYPES|DATA_SET|EXPRESSION_DATA|NONE)

Sets the chart data to show.

network current|[column:value|network name]

showChartLabels true|false

type (RADIAL_HEAT_MAP|HEAT_STRIPS|HEAT_MAP)

Sets the chart type.

enrichmentmap dataset hide

Allows to de-select the data sets to show in an EnrichmentMap network. This command is basically the same as clicking the checkboxes next to the data sets in the main EnrichmentMap panel.

Arguments:

datasets <String>

Comma separated list of dataset names or indexes, for example ‘dataset1,dataset2,3’. The list may also contain positive integers that indicate the index of the dataset in the enrichment map. Alternately use ‘ALL’ to indicate all data sets.

network current|[column:value|network name]

enrichmentmap dataset show

Allows to select the data sets to show in an EnrichmentMap network. This command is basically the same as clicking the checkboxes next to the data sets in the main EnrichmentMap panel.

Arguments:

datasets <String>

Comma separated list of dataset names or indexes, for example ‘dataset1,dataset2,3’. The list may also contain positive integers that indicate the index of the dataset in the enrichment map. Alternately use ‘ALL’ to indicate all data sets.

network current|[column:value|network name]

enrichmentmap export model

Exports the EnrichmentMap data model to a file. Intended mainly for debugging.

Arguments:

file <File>

File used as destination for model JSON. Will be overwritten if it already exists.

network current|[column:value|network name]

enrichmentmap export pdf

Exports the contents of the Heat Map panel to a PDF file.

Arguments:

file <File>

Absolute path to the PDF file to be exported. Will be overwritten if it already exists.

compress (NONE|CLASS_MEDIAN|CLASS_MIN|CLASS_MAX| DATASET_MEDIAN|DATASET_MIN|DATASET_MAX)

network current|[column:value|network name]

openViewer true|false

If true attempts to open a system PDF viewer on the exported file, does not work in headless mode.

operator (union|intersection)

selectedOnly true|false

true (default) for only selected nodes and edges, false for all nodes and edges

showValues true|false

transform (AS_IS|ROW_NORMALIZE|LOG_TRANSFORM)

Additional Command Documentation

CyREST App

The CyREST App is required to call commands via REST. CyREST is installed by default, but it is updated often. If you have any issues you may want to make sure the latest version is installed:

  1. App Manager

    Open the App Manager dialog from the main menu at Apps > App Manager. Then go to the Check For Updates tab. If there is a newer version available it will be listed.

  2. App Store

    CyRest can also be installed or updated from the App Store Website

Swagger Documentation

On-line documentation for EnrichmentMap commands can be accessed from the main menu at Help > Automation > CyREST Command API. This will open a web browser with documentation for all the commands that are available through CyREST. Navigate to the enrichmentmap entry and expand it for detailed documentation on each command.

_images/swagger2.png

Note

For more details on using CyRest see the CyREST Documentation

Command Line Dialog Documentation

Open the Command Dialog from the main menu at Tools > Command Line Dialog.

Type help enrichmentmap to list the available commands provided by EnrichmentMap. To get help on a particular command type, for example the build command, type help enrichmentmap build.

_images/command_dialog.png

Note

For more details on the Command Line Dialog see the Cytoscape User Docs