R/methods.R
createNetwork.RdUser selected enrichment terms are used to create a Cytoscape network where the selected terms and the genes that where part of the enrichment analysis are all represented as nodes. Edges are linking the genes to their terms. The selection of the term can by specifying the source of the terms (GO:MF, REAC, TF, etc.) or by listing the selected term IDs. The network is only generated when there is at least on significant term to graph. When the enrichment analysis contains more than one query, only one query can be selected to generate the network.
createNetwork(
gostObject,
source = c("TERM_ID", "GO:MF", "GO:CC", "GO:BP", "KEGG", "REAC", "TF", "MIRNA", "HPA",
"CORUM", "HP", "WP"),
termIDs = NULL,
removeRoot = TRUE,
query = NULL,
title = "gprofiler network",
collection = "enrichment results",
fileName = "gprofilerNetwork.cx"
)a list created by gprofiler2 that contains
the results from an enrichment analysis.
a character string representing the selected source
that will be used to generate the network. To hand-pick the terms to be
used, "TERM_ID" should be used and the list of selected term IDs should
be passed through the termIDs parameter. The possible sources are
"GO:BP" for Gene Ontology Biological Process, "GO:CC" for Gene Ontology
Cellular Component, "GO:MF" for Gene Ontology Molecular Function,
"KEGG" for Kegg, "REAC" for Reactome, "TF" for TRANSFAC, "MIRNA" for
miRTarBase, "CORUM" for CORUM database, "HP" for Human phenotype ontology
and "WP" for WikiPathways. Default: "TERM_ID".
a vector of character strings that contains the
term IDS retained for the creation of the network. Default: NULL.
a logical that specified if the root terms of
the selected source should be removed (when present). Default: TRUE.
a character string that specified the retained query to
generate the network. When NULL, the query present in the result
is retained; NULL cannot be used when more than one query is present.
Default: NULL.
a character string representing the name assigned to
the network. Default: "gprofiler network".
a character string representing the collection
name assigned to the network. Default: "enrichment results".
a character string representing the name of the
CX JSON file that is created when Cytoscape is not running. The name
must have a '.cx' extension.
Default: "gprofilerNetwork_01.cx".
TRUE
## Loading dataset containing result from an enrichment analysis done with
## gprofiler2
data(parentalNapaVsDMSOEnrichment)
## Some of the enrichment results present in the dataset
head(parentalNapaVsDMSOEnrichment$result)
#> query significant p_value term_size query_size
#> 1 parental_napa_vs_DMSO TRUE 2.198177e-11 3187 157
#> 2 parental_napa_vs_DMSO TRUE 2.139995e-10 1238 157
#> 3 parental_napa_vs_DMSO TRUE 2.848209e-10 3583 157
#> 4 parental_napa_vs_DMSO TRUE 8.790372e-10 48 157
#> 5 parental_napa_vs_DMSO TRUE 3.046614e-09 4216 157
#> 6 parental_napa_vs_DMSO TRUE 3.550218e-09 4119 157
#> intersection_size precision recall term_id source
#> 1 59 0.37579618 0.01851271 GO:0048523 GO:BP
#> 2 35 0.22292994 0.02827141 GO:0008219 GO:BP
#> 3 61 0.38853503 0.01702484 GO:0048519 GO:BP
#> 4 10 0.06369427 0.20833333 GO:0070059 GO:BP
#> 5 65 0.41401274 0.01541746 GO:0080090 GO:BP
#> 6 64 0.40764331 0.01553775 GO:0051171 GO:BP
#> term_name
#> 1 negative regulation of cellular process
#> 2 cell death
#> 3 negative regulation of biological process
#> 4 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
#> 5 regulation of primary metabolic process
#> 6 regulation of nitrogen compound metabolic process
#> effective_domain_size source_order parents
#> 1 24022 13544 GO:00099....
#> 2 24022 3218 GO:0009987
#> 3 24022 13540 GO:00081....
#> 4 24022 16817 GO:00349....
#> 5 24022 18790 GO:00192....
#> 6 24022 14316 GO:00068....
#> evidence_codes
#> 1 IMP,IDA IGI IBA,IDA,IDA TAS,IDA IMP TAS,IDA,IDA IMP IBA NAS,ISS,ISS,IDA IMP ISS IBA,ISS,IDA IMP ISS,IDA IMP IGI IEP IBA TAS,IDA,TAS,IDA IMP,IDA IMP ISS,IGI ISS,ISS,IMP,IMP ISS IBA,IDA IBA NAS,IDA IGI TAS,IBA,IDA IBA,IDA TAS,IDA IMP IBA TAS,ISS,IDA ISS,IDA,IDA,IBA,IDA IMP IBA TAS,IDA,IDA,IDA IMP ISS IBA IC,IMP ISS IBA,ISS,IDA IMP IBA,ISS,ISS,IDA,IMP,TAS,IDA IMP IGI ISS ISO IBA,IBA,IMP,IDA IMP IBA,IDA ISS IBA,IBA,IMP TAS,NAS,IDA,ISS,IDA ISS NAS,IDA IMP TAS,IDA IMP TAS,IDA ISS ISO TAS,IBA
#> 2 IDA IGI IBA,TAS,IDA,IMP,IDA IMP IGI ISS IBA TAS,IDA NAS,ISS,ISS,IMP,TAS,IDA,TAS,IMP,IGI ISS TAS,IMP,IMP,IDA,IMP,TAS,IDA IMP TAS,IMP,IMP ISS TAS,NAS,IDA IMP IGI IBA TAS,IMP,IDA ISS,ISS,TAS,TAS,IDA IMP ISS IBA TAS IC,IMP,TAS,IDA IMP TAS,IDA IMP TAS,IBA
#> 3 IMP,IDA IGI IBA,IDA,IDA TAS,IDA IMP TAS,IDA IMP,ISS,IDA IMP IBA NAS,ISS,ISS,IDA IMP ISS IBA,ISS,IDA IMP ISS,IDA IMP IGI IEP ISS IBA TAS,IDA,TAS,IDA IMP,IDA IMP ISS TAS,IGI ISS,ISS,IMP,IMP ISS IBA,IDA IBA NAS,IDA IGI TAS,IBA,IDA IBA,IDA TAS,IDA IMP IBA TAS,ISS,IDA ISS,IDA,IDA,IBA,IDA IMP IBA TAS,IDA,IDA,IMP,IDA IMP ISS IBA IC,IMP ISS IBA,ISS,IDA IMP IBA,IGI ISS,ISS,IDA,IMP,TAS,IDA IMP IGI ISS ISO IBA,IBA,IMP,IDA IMP IBA,IDA ISS IBA,IBA,IMP TAS,NAS,IDA,ISS,IDA ISS NAS,IDA IMP TAS,IDA IMP TAS,IDA ISS ISO TAS,IBA
#> 4 IDA IBA,TAS,IDA ISS IBA TAS,ISS,IMP,TAS,TAS,TAS,IDA IMP IBA TAS IC,IDA
#> 5 IDA IMP IBA,IDA IBA,IDA IBA TAS IC,ISS,IDA IBA,IDA,IDA ISS IBA,IBA,IPI,IDA IMP IBA NAS,ISS,IDA ISS IBA,IBA,IDA,IDA IMP IGI ISS IBA,IDA ISS IBA,IDA IBA,IDA IMP ISS IBA,IDA IMP IEP IBA TAS,IBA TAS,IDA IMP IBA,IDA IMP ISS,IDA IMP ISS ISO IBA NAS IC,IMP,IDA IMP,NAS,IDA IBA,IDA IMP IGI ISS IBA NAS,IDA,IDA IMP IBA,IDA,ISS,ISS IBA,TAS,IBA,IDA,IDA IBA,IDA,IDA ISS IBA NAS,IDA,IMP,IDA IMP ISS IBA,IBA,ISS IBA,IDA IGI ISS,IDA IMP IGI ISS IBA TAS NAS,IBA,IDA IBA TAS NAS,EXP IDA IMP ISS IBA NAS,IDA IMP ISS IBA,IDA IMP IGI ISS ISO IBA TAS NAS,IBA,IBA,IDA IBA,IDA ISS,IMP,IDA IBA NAS,TAS,IBA,IMP ISS IBA NAS,IDA IMP IBA,IDA IMP IBA,IDA IMP IGI ISS ISO IBA TAS NAS,IBA,IBA
#> 6 IDA IMP IBA,IDA IBA,IDA IBA TAS IC,ISS,IDA IBA,IDA,IDA ISS IBA,IBA,IPI,IDA IMP IBA NAS,ISS,IDA ISS IBA,IBA,IDA,IDA IMP IGI ISS IBA,IDA ISS IBA,IDA IBA,IDA IMP ISS IBA,IDA IMP IEP IBA TAS,IBA TAS,IDA IMP IBA,IDA IMP ISS,IDA IMP ISS ISO IBA NAS IC,IMP,IDA IMP,NAS,IDA IBA,IDA IMP IGI ISS IBA NAS,IDA,IDA IMP IBA,IDA,ISS,ISS IBA,IBA,IDA,IDA IBA,IDA,IDA ISS IBA NAS,IDA,IMP,IDA IMP ISS IBA,IBA,ISS IBA,IDA IGI ISS,IDA IMP IGI ISS IBA TAS NAS,IBA,IDA IBA TAS NAS,EXP IDA IMP ISS IBA NAS,IDA IMP ISS IBA,IDA IMP IGI ISS ISO IBA TAS NAS,IBA,IBA,IDA IBA,IDA ISS,IMP,IDA IBA NAS,TAS,IBA,IMP ISS IBA NAS,IDA IMP IBA,IDA IMP IBA,IDA IMP IGI ISS ISO IBA TAS NAS,IBA,IBA
#> intersection
#> 1 ENSG00000007944,ENSG00000051108,ENSG00000059728,ENSG00000087074,ENSG00000100292,ENSG00000105327,ENSG00000113916,ENSG00000116741,ENSG00000119508,ENSG00000120129,ENSG00000123358,ENSG00000124216,ENSG00000124762,ENSG00000125266,ENSG00000125740,ENSG00000125812,ENSG00000128016,ENSG00000128272,ENSG00000128590,ENSG00000128965,ENSG00000130766,ENSG00000133639,ENSG00000136826,ENSG00000138166,ENSG00000140961,ENSG00000141232,ENSG00000141582,ENSG00000142178,ENSG00000143878,ENSG00000148926,ENSG00000157557,ENSG00000158050,ENSG00000159388,ENSG00000162772,ENSG00000163273,ENSG00000163874,ENSG00000164056,ENSG00000164920,ENSG00000168140,ENSG00000169242,ENSG00000172216,ENSG00000172602,ENSG00000173334,ENSG00000173530,ENSG00000175197,ENSG00000177873,ENSG00000179388,ENSG00000183508,ENSG00000183691,ENSG00000184545,ENSG00000184557,ENSG00000185022,ENSG00000197019,ENSG00000198576,ENSG00000204103,ENSG00000204388,ENSG00000204389,ENSG00000245848,ENSG00000256223
#> 2 ENSG00000051108,ENSG00000087074,ENSG00000099860,ENSG00000100292,ENSG00000105327,ENSG00000113916,ENSG00000119508,ENSG00000120738,ENSG00000124216,ENSG00000124762,ENSG00000125266,ENSG00000125657,ENSG00000128016,ENSG00000128272,ENSG00000128965,ENSG00000133639,ENSG00000136826,ENSG00000140961,ENSG00000141582,ENSG00000141682,ENSG00000142178,ENSG00000143878,ENSG00000144655,ENSG00000153094,ENSG00000162772,ENSG00000163874,ENSG00000170345,ENSG00000172216,ENSG00000173530,ENSG00000175197,ENSG00000179388,ENSG00000184557,ENSG00000204388,ENSG00000204389,ENSG00000241839
#> 3 ENSG00000007944,ENSG00000051108,ENSG00000059728,ENSG00000087074,ENSG00000100292,ENSG00000105327,ENSG00000113369,ENSG00000113916,ENSG00000116741,ENSG00000119508,ENSG00000120129,ENSG00000123358,ENSG00000124216,ENSG00000124762,ENSG00000125266,ENSG00000125740,ENSG00000125812,ENSG00000128016,ENSG00000128272,ENSG00000128590,ENSG00000128965,ENSG00000130766,ENSG00000133639,ENSG00000136826,ENSG00000138166,ENSG00000140961,ENSG00000141232,ENSG00000141582,ENSG00000142178,ENSG00000143878,ENSG00000148926,ENSG00000157557,ENSG00000158050,ENSG00000159388,ENSG00000162772,ENSG00000163273,ENSG00000163659,ENSG00000163874,ENSG00000164056,ENSG00000164920,ENSG00000168140,ENSG00000169242,ENSG00000172216,ENSG00000172602,ENSG00000173334,ENSG00000173530,ENSG00000175197,ENSG00000177873,ENSG00000179388,ENSG00000183508,ENSG00000183691,ENSG00000184545,ENSG00000184557,ENSG00000185022,ENSG00000197019,ENSG00000198576,ENSG00000204103,ENSG00000204388,ENSG00000204389,ENSG00000245848,ENSG00000256223
#> 4 ENSG00000051108,ENSG00000087074,ENSG00000105327,ENSG00000128272,ENSG00000128965,ENSG00000141682,ENSG00000153094,ENSG00000172216,ENSG00000175197,ENSG00000204389
#> 5 ENSG00000051108,ENSG00000059728,ENSG00000087074,ENSG00000100292,ENSG00000102554,ENSG00000103044,ENSG00000105327,ENSG00000113070,ENSG00000113369,ENSG00000113916,ENSG00000116741,ENSG00000119508,ENSG00000119630,ENSG00000120129,ENSG00000120738,ENSG00000122877,ENSG00000123358,ENSG00000124216,ENSG00000124762,ENSG00000125740,ENSG00000125812,ENSG00000128016,ENSG00000128272,ENSG00000128965,ENSG00000130766,ENSG00000133639,ENSG00000135625,ENSG00000136826,ENSG00000141232,ENSG00000141582,ENSG00000141682,ENSG00000142178,ENSG00000144655,ENSG00000148926,ENSG00000152433,ENSG00000153094,ENSG00000157557,ENSG00000159388,ENSG00000162772,ENSG00000162783,ENSG00000163659,ENSG00000163874,ENSG00000164056,ENSG00000164920,ENSG00000169242,ENSG00000170345,ENSG00000170684,ENSG00000171223,ENSG00000172216,ENSG00000173334,ENSG00000175197,ENSG00000177873,ENSG00000179388,ENSG00000183508,ENSG00000183691,ENSG00000184557,ENSG00000185022,ENSG00000197019,ENSG00000197566,ENSG00000204103,ENSG00000204388,ENSG00000204389,ENSG00000245848,ENSG00000256223,ENSG00000257446
#> 6 ENSG00000051108,ENSG00000059728,ENSG00000087074,ENSG00000100292,ENSG00000102554,ENSG00000103044,ENSG00000105327,ENSG00000113070,ENSG00000113369,ENSG00000113916,ENSG00000116741,ENSG00000119508,ENSG00000119630,ENSG00000120129,ENSG00000120738,ENSG00000122877,ENSG00000123358,ENSG00000124216,ENSG00000124762,ENSG00000125740,ENSG00000125812,ENSG00000128016,ENSG00000128272,ENSG00000128965,ENSG00000130766,ENSG00000133639,ENSG00000135625,ENSG00000136826,ENSG00000141232,ENSG00000141582,ENSG00000141682,ENSG00000142178,ENSG00000144655,ENSG00000152433,ENSG00000153094,ENSG00000157557,ENSG00000159388,ENSG00000162772,ENSG00000162783,ENSG00000163659,ENSG00000163874,ENSG00000164056,ENSG00000164920,ENSG00000169242,ENSG00000170345,ENSG00000170684,ENSG00000171223,ENSG00000172216,ENSG00000173334,ENSG00000175197,ENSG00000177873,ENSG00000179388,ENSG00000183508,ENSG00000183691,ENSG00000184557,ENSG00000185022,ENSG00000197019,ENSG00000197566,ENSG00000204103,ENSG00000204388,ENSG00000204389,ENSG00000245848,ENSG00000256223,ENSG00000257446
## Create network for Gene Ontology - Molecular Function related results
## in Cytoscape (when the application is opened)
## Otherwise, create a CX file in the temporary directory
## The file can be opened in Cytoscape
createNetwork(gostObject=parentalNapaVsDMSOEnrichment, source="KEGG",
removeRoot=FALSE, title="KEGG Graph",
fileName=file.path(tempdir(), "KEGG_demo.cx"))
#> Oh no! I can't find Cytoscape. RCy3 can not continue!
#> Please check that Cytoscape is running, CyREST is installed and your base.url parameter is correct.
#> Unable to connect to Cytoscape.
#> CX JSON file will be created.
#> Preparing information for generating CX JSON file.
#> CX JSON file "/tmp/Rtmpsp1G54/KEGG_demo.cx" has been created.
#> [1] TRUE