bioconductor v3.9.0 ClusterProfiler

This package implements methods to analyze and visualize

Link to this section Summary

Functions

Datasets gcSample contains a sample of gene clusters.

GSEA

Gff2GeneTable

KEGG_path2extid

bitr

bitr_kegg

browseKEGG

buildGOmap

statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.

Compare gene clusters functional profile

Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.

download_KEGG

dropGO

enrichDAVID

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.

KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.

enricher

fortify

get GOIDs at a specific level

go2ont

go2term

gofilter

Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.

Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.

gseGO

gseKEGG

gseMKEGG

idType

ko2name

merge_result

plotGOgraph

plotting-clusterProfile

read.gmt

Objects exported from other packages

search_kegg_organism

simplify method

uniprot_get

viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway

Link to this section Functions

Datasets gcSample contains a sample of gene clusters.

Description

Datasets gcSample contains a sample of gene clusters.

Datasets kegg_species contains kegg species information

GSEA

Description

a universal gene set enrichment analysis tools

Usage

GSEA(geneList, exponent = 1, nPerm = 1000, minGSSize = 10,
  maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH",
  TERM2GENE, TERM2NAME = NA, verbose = TRUE, seed = FALSE,
  by = "fgsea")

Arguments

ArgumentDescription
geneListorder ranked geneList
exponentweight of each step
nPermnumber of permutations
minGSSizeminimal size of each geneSet for analyzing
maxGSSizemaximal size of genes annotated for testing
pvalueCutoffpvalue cutoff
pAdjustMethodp value adjustment method
TERM2GENEuser input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
TERM2NAMEuser input of TERM TO NAME mapping, a data.frame of 2 column with term and name
verboselogical
seedlogical
byone of 'fgsea' or 'DOSE'

Value

gseaResult object

Author

Guangchuang Yu

Link to this function

Gff2GeneTable()

Gff2GeneTable

Description

read GFF file and build gene information table

Usage

Gff2GeneTable(gffFile, compress = TRUE)

Arguments

ArgumentDescription
gffFileGFF file
compresscompress file or not

Details

given a GFF file, this function extracts information from it and save it in working directory

Value

file save.

Author

Yu Guangchuang

Link to this function

KEGG_path2extid()

KEGG_path2extid

Description

query all genes in a KEGG pathway or module

Usage

KEGG_path2extid(keggID, species = sub("\d+$", "", keggID),
  keggType = "Path", keyType = "kegg")

Arguments

ArgumentDescription
keggIDKEGG ID, path or module ID
speciesspecies
keggTypeone of 'Path' or 'Module'
keyTypeKEGG gene type, one of "ncbi-proteinid", "ncbi-geneid", "uniprot", or "kegg"

Value

extid vector

Author

guangchuang yu

bitr

Description

Biological Id TRanslator

Usage

bitr(geneID, fromType, toType, OrgDb, drop = TRUE)

Arguments

ArgumentDescription
geneIDinput gene id
fromTypeinput id type
toTypeoutput id type
OrgDbannotation db
dropdrop NA or not

Value

data.frame

Author

Guangchuang Yu

bitr_kegg

Description

convert biological ID using KEGG API

Usage

bitr_kegg(geneID, fromType, toType, organism, drop = TRUE)

Arguments

ArgumentDescription
geneIDinput gene id
fromTypeinput id type
toTypeoutput id type
organismsupported organism, can be search using search_kegg_organism function
dropdrop NA or not

Value

data.frame

Author

Guangchuang Yu

browseKEGG

Description

open KEGG pathway with web browser

Usage

browseKEGG(x, pathID)

Arguments

ArgumentDescription
xan instance of enrichResult or gseaResult
pathIDpathway ID

Value

url

Author

Guangchuang Yu

buildGOmap

Description

building GO mapping files

Usage

buildGOmap(gomap)

Arguments

ArgumentDescription
gomapdata.frame with two columns of GO and gene ID

Details

provided by a data.frame of GO (column 1) and gene (column 2) direct annotation this function will building gene to GO and GO to gene mapping, with directly and undirectly (ancestor GO term) annotation.

Value

data.frame, GO annotation with indirect annotation

Author

Yu Guangchuang

Link to this function

clusterProfiler_package()

statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.

Description

statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.

Link to this function

compareCluster()

Compare gene clusters functional profile

Description

Given a list of gene set, this function will compute profiles of each gene cluster.

Usage

compareCluster(geneClusters, fun = "enrichGO", data = "", ...)

Arguments

ArgumentDescription
geneClustersa list of entrez gene id. Alternatively, a formula of type Entrez~group
funOne of "groupGO", "enrichGO", "enrichKEGG", "enrichDO" or "enrichPathway" .
dataif geneClusters is a formula, the data from which the clusters must be extracted.
...Other arguments.

Value

A clusterProfResult instance.

Seealso

compareClusterResult-class , groupGO enrichGO

Author

Guangchuang Yu https://guangchuangyu.github.io

Examples

data(gcSample)
xx <- compareCluster(gcSample, fun="enrichKEGG",
organism="hsa", pvalueCutoff=0.05)
as.data.frame(xx)
# plot(xx, type="dot", caption="KEGG Enrichment Comparison")

## formula interface
mydf <- data.frame(Entrez=c('1', '100', '1000', '100101467',
'100127206', '100128071'),
group = c('A', 'A', 'A', 'B', 'B', 'B'),
othergroup = c('good', 'good', 'bad', 'bad', 'good', 'bad'))
xx.formula <- compareCluster(Entrez~group, data=mydf,
fun='groupGO', OrgDb='org.Hs.eg.db')
as.data.frame(xx.formula)

## formula interface with more than one grouping variable
xx.formula.twogroups <- compareCluster(Entrez~group+othergroup, data=mydf,
fun='groupGO', OrgDb='org.Hs.eg.db')
as.data.frame(xx.formula.twogroups)
Link to this function

compareClusterResult_class()

Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.

Description

Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.

Seealso

groupGOResult enrichResult compareCluster

Author

Guangchuang Yu https://guangchuangyu.github.io

Link to this function

dotplot_methods()

dotplot

Description

dot plot method

Usage

list(list("dotplot"), list("compareClusterResult"))(object, x = ~Cluster,
  color = "p.adjust", showCategory = 5, split = NULL,
  font.size = 12, title = "", by = "geneRatio", includeAll = TRUE)

Arguments

ArgumentDescription
objectcompareClusterResult object
xx variable
colorone of pvalue or p.adjust
showCategorycategory numbers
splitONTOLOGY or NULL
font.sizefont size
titlefigure title
byone of geneRatio, Percentage or count
includeAlllogical
Link to this function

download_KEGG()

download_KEGG

Description

download the latest version of KEGG pathway/module

Usage

download_KEGG(species, keggType = "KEGG", keyType = "kegg")

Arguments

ArgumentDescription
speciesspecies
keggTypeone of 'KEGG' or 'MKEGG'
keyTypesupported keyType, see bitr_kegg

Value

list

Author

Guangchuang Yu

dropGO

Description

drop GO term of specific level or specific terms (mostly too general).

Usage

dropGO(x, level = NULL, term = NULL)

Arguments

ArgumentDescription
xan instance of 'enrichResult' or 'compareClusterResult'
levelGO level
termGO term

Value

modified version of x

Author

Guangchuang Yu

enrichDAVID

Description

enrichment analysis by DAVID

Usage

enrichDAVID(gene, idType = "ENTREZ_GENE_ID", universe, minGSSize = 10,
  maxGSSize = 500, annotation = "GOTERM_BP_FAT", pvalueCutoff = 0.05,
  pAdjustMethod = "BH", qvalueCutoff = 0.2, species = NA, david.user)

Arguments

ArgumentDescription
geneinput gene
idTypeid type
universebackground genes
minGSSizeminimal size of genes annotated for testing
maxGSSizemaximal size of genes annotated for testing
annotationdavid annotation
pvalueCutoffpvalueCutoff
pAdjustMethodone of "BH" and "bonferroni"
qvalueCutoffqvalutCutoff
speciesspecies
david.userdavid user

Value

A enrichResult instance

Author

Guangchuang Yu

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

Description

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

Usage

enrichGO(gene, OrgDb, keyType = "ENTREZID", ont = "MF",
  pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
  qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500,
  readable = FALSE, pool = FALSE)

Arguments

ArgumentDescription
genea vector of entrez gene id.
OrgDbOrgDb
keyTypekeytype of input gene
ontOne of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
pvalueCutoffCutoff value of pvalue.
pAdjustMethodone of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universebackground genes
qvalueCutoffqvalue cutoff
minGSSizeminimal size of genes annotated by Ontology term for testing.
maxGSSizemaximal size of genes annotated for testing
readablewhether mapping gene ID to gene Name
poolIf ont='ALL', whether pool 3 GO sub-ontologies

Value

An enrichResult instance.

Seealso

enrichResult-class , compareCluster

Author

Guangchuang Yu https://guangchuangyu.github.io

Examples

data(geneList, package = "DOSE")
de <- names(geneList)[1:100]
yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
head(yy)

KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.

Description

KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.

Usage

enrichKEGG(gene, organism = "hsa", keyType = "kegg",
  pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
  minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2,
  use_internal_data = FALSE)

Arguments

ArgumentDescription
genea vector of entrez gene id.
organismsupported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
keyTypeone of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
pvalueCutoffCutoff value of pvalue.
pAdjustMethodone of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universebackground genes
minGSSizeminimal size of genes annotated by Ontology term for testing.
maxGSSizemaximal size of genes annotated for testing
qvalueCutoffqvalue cutoff
use_internal_datalogical, use KEGG.db or latest online KEGG data

Value

A enrichResult instance.

Seealso

enrichResult-class , compareCluster

Author

Guangchuang Yu http://ygc.name

Examples

data(geneList, package='DOSE')
de <- names(geneList)[1:100]
yy <- enrichKEGG(de, pvalueCutoff=0.01)
head(yy)

KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.

Description

KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.

Usage

enrichMKEGG(gene, organism = "hsa", keyType = "kegg",
  pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
  minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2)

Arguments

ArgumentDescription
genea vector of entrez gene id.
organismsupported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
keyTypeone of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
pvalueCutoffCutoff value of pvalue.
pAdjustMethodone of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universebackground genes
minGSSizeminimal size of genes annotated by Ontology term for testing.
maxGSSizemaximal size of genes annotated for testing
qvalueCutoffqvalue cutoff

Value

A enrichResult instance.

enricher

Description

A universal enrichment analyzer

Usage

enricher(gene, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe,
  minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2, TERM2GENE,
  TERM2NAME = NA)

Arguments

ArgumentDescription
genea vector of gene id
pvalueCutoffpvalue cutoff
pAdjustMethodone of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universebackground genes
minGSSizeminimal size of genes annotated for testing
maxGSSizemaximal size of genes annotated for testing
qvalueCutoffqvalue cutoff
TERM2GENEuser input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
TERM2NAMEuser input of TERM TO NAME mapping, a data.frame of 2 column with term and name

Value

A enrichResult instance

Author

Guangchuang Yu

fortify

Description

convert compareClusterResult to a data.frame that ready for plot

Usage

list(list("fortify"), list("compareClusterResult"))(model, data, showCategory = 5,
  by = "geneRatio", split = NULL, includeAll = TRUE)

Arguments

ArgumentDescription
modelcompareClusterResult object
datanot use here
showCategorycategory numbers
byone of geneRatio, Percentage or count
splitONTOLOGY or NULL
includeAlllogical

Value

data.frame

Author

Guangchuang Yu

get GOIDs at a specific level

Description

query GOIDs at a specific level.

Usage

getGOLevel(ont, level)

Arguments

ArgumentDescription
ontOntology
levelGO level

Value

a vector of GOIDs

Author

Guangchuang Yu http://guangchuangyu.github.io

go2ont

Description

convert goid to ontology (BP, CC, MF)

Usage

go2ont(goid)

Arguments

ArgumentDescription
goida vector of GO IDs

Value

data.frame

Author

Guangchuang Yu

go2term

Description

convert goid to descriptive term

Usage

go2term(goid)

Arguments

ArgumentDescription
goida vector of GO IDs

Value

data.frame

Author

Guangchuang Yu

gofilter

Description

filter GO enriched result at specific level

Usage

gofilter(x, level = 4)

Arguments

ArgumentDescription
xoutput from enrichGO or compareCluster
levelGO level

Value

updated object

Author

Guangchuang Yu

Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.

Description

Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.

Usage

groupGO(gene, OrgDb, keyType = "ENTREZID", ont = "CC", level = 2,
  readable = FALSE)

Arguments

ArgumentDescription
genea vector of entrez gene id.
OrgDbOrgDb
keyTypekey type of input gene
ontOne of "MF", "BP", and "CC" subontologies.
levelSpecific GO Level.
readableif readable is TRUE, the gene IDs will mapping to gene symbols.

Value

A groupGOResult instance.

Seealso

groupGOResult-class , compareCluster

Author

Guangchuang Yu http://ygc.name

Examples

data(gcSample)
yy <- groupGO(gcSample[[1]], 'org.Hs.eg.db', ont="BP", level=2)
head(summary(yy))
#plot(yy)
Link to this function

groupGOResult_class()

Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.

Description

Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.

Seealso

compareClusterResult compareCluster groupGO

Author

Guangchuang Yu https://guangchuangyu.github.io

gseGO

Description

Gene Set Enrichment Analysis of Gene Ontology

Usage

gseGO(geneList, ont = "BP", OrgDb, keyType = "ENTREZID",
  exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500,
  pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
  seed = FALSE, by = "fgsea")

Arguments

ArgumentDescription
geneListorder ranked geneList
ontone of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
OrgDbOrgDb
keyTypekeytype of gene
exponentweight of each step
nPermpermutation numbers
minGSSizeminimal size of each geneSet for analyzing
maxGSSizemaximal size of genes annotated for testing
pvalueCutoffpvalue Cutoff
pAdjustMethodpvalue adjustment method
verboseprint message or not
seedlogical
byone of 'fgsea' or 'DOSE'

Value

gseaResult object

Author

Yu Guangchuang

gseKEGG

Description

Gene Set Enrichment Analysis of KEGG

Usage

gseKEGG(geneList, organism = "hsa", keyType = "kegg", exponent = 1,
  nPerm = 1000, minGSSize = 10, maxGSSize = 500,
  pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
  use_internal_data = FALSE, seed = FALSE, by = "fgsea")

Arguments

ArgumentDescription
geneListorder ranked geneList
organismsupported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
keyTypeone of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
exponentweight of each step
nPermpermutation numbers
minGSSizeminimal size of each geneSet for analyzing
maxGSSizemaximal size of genes annotated for testing
pvalueCutoffpvalue Cutoff
pAdjustMethodpvalue adjustment method
verboseprint message or not
use_internal_datalogical, use KEGG.db or latest online KEGG data
seedlogical
byone of 'fgsea' or 'DOSE'

Value

gseaResult object

Author

Yu Guangchuang

gseMKEGG

Description

Gene Set Enrichment Analysis of KEGG Module

Usage

gseMKEGG(geneList, organism = "hsa", keyType = "kegg", exponent = 1,
  nPerm = 1000, minGSSize = 10, maxGSSize = 500,
  pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
  seed = FALSE, by = "fgsea")

Arguments

ArgumentDescription
geneListorder ranked geneList
organismsupported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
keyTypeone of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
exponentweight of each step
nPermpermutation numbers
minGSSizeminimal size of each geneSet for analyzing
maxGSSizemaximal size of genes annotated for testing
pvalueCutoffpvalue Cutoff
pAdjustMethodpvalue adjustment method
verboseprint message or not
seedlogical
byone of 'fgsea' or 'DOSE'

Value

gseaResult object

Author

Yu Guangchuang

idType

Description

list ID types supported by annoDb

Usage

idType(OrgDb = "org.Hs.eg.db")

Arguments

ArgumentDescription
OrgDbannotation db

Value

character vector

Author

Guangchuang Yu

ko2name

Description

convert ko ID to descriptive name

Usage

ko2name(ko)

Arguments

ArgumentDescription
koko ID

Value

data.frame

Author

guangchuang yu

merge_result

Description

merge a list of enrichResult objects to compareClusterResult

Usage

merge_result(enrichResultList)

Arguments

ArgumentDescription
enrichResultLista list of enrichResult objects

Value

a compareClusterResult instance

Author

Guangchuang Yu

plotGOgraph

Description

plot GO graph

Usage

plotGOgraph(x, firstSigNodes = 10, useInfo = "all", sigForAll = TRUE,
  useFullNames = TRUE, ...)

Arguments

ArgumentDescription
xoutput of enrichGO or gseGO
firstSigNodesnumber of significant nodes (retangle nodes in the graph)
useInfoadditional info
sigForAllif TRUE the score/p-value of all nodes in the DAG is shown, otherwise only score will be shown
useFullNameslogical
...additional parameter of showSigOfNodes, please refer to topGO

Value

GO DAG graph

Author

Guangchuang Yu

Link to this function

plottingclusterProfile()

plotting-clusterProfile

Description

Internal plot function for plotting compareClusterResult

Usage

plotting.clusterProfile(clProf.reshape.df, x = ~Cluster, type = "dot",
  colorBy = "p.adjust", by = "geneRatio", title = "",
  font.size = 12)

Arguments

ArgumentDescription
clProf.reshape.dfdata frame of compareCluster result
xx variable
typeone of dot and bar
colorByone of pvalue or p.adjust
byone of percentage and count
titlegraph title
font.sizegraph font size

Value

ggplot object

Author

Guangchuang Yu https://guangchuangyu.github.io

read.gmt

Description

parse gmt file to a data.frame

Usage

read.gmt(gmtfile)

Arguments

ArgumentDescription
gmtfilegmt file

Value

data.frame

Author

Guangchuang Yu

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

list(" ", " ", list(list("DOSE"), list(list(list("geneID")), ", ", list(list("geneInCategory")), ", ", list(list("gsfilter")), ", ", list(list("setReadable")))), " ", " ", " ", list(list("enrichplot"), list(list(list("cnetplot")), ", ", list(list("dotplot")), ", ", list(list("emapplot")), ", ", list(list("goplot")), ", ", list(list("gseaplot")), ", ", list(list("heatplot")), ", ", list(list("ridgeplot")))), " ")

Link to this function

search_kegg_organism()

search_kegg_organism

Description

search kegg organism, listed in http://www.genome.jp/kegg/catalog/org_list.html

Usage

search_kegg_organism(str, by = "scientific_name", ignore.case = FALSE)

Arguments

ArgumentDescription
strstring
byone of 'kegg.code', 'scientific_name' and 'common_name'
ignore.caseTRUE or FALSE

Value

data.frame

Author

Guangchuang Yu

Link to this function

simplify_methods()

simplify method

Description

simplify output from enrichGO and gseGO by removing redundancy of enriched GO terms

simplify output from compareCluster by removing redundancy of enriched GO terms

Usage

list(list("simplify"), list("enrichResult"))(x, cutoff = 0.7, by = "p.adjust",
  select_fun = min, measure = "Wang", semData = NULL)
list(list("simplify"), list("gseaResult"))(x, cutoff = 0.7, by = "p.adjust",
  select_fun = min, measure = "Wang", semData = NULL)
list(list("simplify"), list("compareClusterResult"))(x, cutoff = 0.7,
  by = "p.adjust", select_fun = min, measure = "Wang",
  semData = NULL)

Arguments

ArgumentDescription
xoutput of enrichGO
cutoffsimilarity cutoff
byfeature to select representative term, selected by 'select_fun' function
select_funfunction to select feature passed by 'by' parameter
measuremethod to measure similarity
semDataGOSemSimDATA object

Value

updated enrichResult object

updated compareClusterResult object

Author

Guangchuang Yu

Gwang-Jin Kim and Guangchuang Yu

Guangchuang Yu

References

issue #28 https://github.com/GuangchuangYu/clusterProfiler/issues/28

issue #162 https://github.com/GuangchuangYu/clusterProfiler/issues/162

uniprot_get

Description

retreve annotation data from uniprot

Usage

uniprot_get(taxID)

Arguments

ArgumentDescription
taxIDtaxonomy ID

Value

gene table data frame

Author

guangchuang yu

viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway

Description

viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway

Usage

viewKEGG(obj, pathwayID, foldChange, color.low = "green",
  color.high = "red", kegg.native = TRUE,
  out.suffix = "clusterProfiler")

Arguments

ArgumentDescription
objenrichResult object
pathwayIDpathway ID or index
foldChangefold change values
color.lowcolor of low foldChange genes
color.highcolor of high foldChange genes
kegg.nativelogical
out.suffixsuffix of output file

References

Luo et al. (2013) Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics (Oxford, England), 29:14 1830--1831, 2013. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/content/abstract/29/14/1830.abstract PMID: 23740750