Filtering Clusterprofiler Result Object
1
0
Entering edit mode
jms2520 • 0
@3184ac53
Last seen 4 days ago
United States

Hello!

I am running cluster profiler gseGO() function and there are a number of significant GO terms. When I print out the entire list of GO terms I see that many of the significant terms are related to inflammation and fall into similar pathways and categories but there are also unrelated terms. I would like to create a dotplot to visualize specifically these inflammation related terms in one graph. Is it possible to filter the GSEresult object for specific GO terms to put into one graph?

clusterProfiler • 67 views
ADD COMMENT
0
Entering edit mode
Guido Hooiveld ★ 3.2k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …

You can make use of the showCategory argument to specify the descriptions of the GO categories you would like to visualize.

> library(clusterProfiler)
> library(DOSE)
> data(geneList)
> 
> out.test <- gseGO(geneList, ont = "BP", OrgDb=org.Hs.eg.db, eps=0)
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
> 
> # check
> head(as.data.frame(out.test))
                   ID                          Description setSize
GO:0007059 GO:0007059               chromosome segregation     248
GO:0000819 GO:0000819         sister chromatid segregation     156
GO:0000280 GO:0000280                     nuclear division     323
GO:0000070 GO:0000070 mitotic sister chromatid segregation     135
GO:0051301 GO:0051301                        cell division     470
GO:0098813 GO:0098813       nuclear chromosome segregation     200
           enrichmentScore      NES       pvalue     p.adjust      qvalues rank
GO:0007059       0.5963868 2.750921 3.609720e-25 2.093999e-21 1.691249e-21 1374
GO:0000819       0.6721567 2.911727 1.375193e-24 2.659166e-21 2.147714e-21  532
GO:0000280       0.5439154 2.585275 1.041198e-24 2.659166e-21 2.147714e-21 1246
GO:0000070       0.6901685 2.946863 2.251548e-23 3.265307e-20 2.637274e-20  532
GO:0051301       0.4757701 2.324002 4.839659e-23 5.614972e-20 4.535015e-20 1108
GO:0098813       0.6123682 2.765219 1.242271e-22 1.029488e-19 8.314808e-20  449
                             leading_edge
GO:0007059 tags=29%, list=11%, signal=26%
GO:0000819  tags=28%, list=4%, signal=27%
GO:0000280 tags=26%, list=10%, signal=24%
GO:0000070  tags=30%, list=4%, signal=29%
GO:0051301  tags=21%, list=9%, signal=20%
GO:0098813  tags=22%, list=4%, signal=22%
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          core_enrichment
GO:0007059                                                                                                                                          55143/991/9493/1062/10403/7153/23397/9787/11065/55355/220134/51203/10460/4751/55839/4085/81930/81620/332/7272/64151/9212/9319/9055/3833/146909/891/24137/9232/9928/11004/990/5347/29127/26255/701/11130/57405/10615/1894/79075/9700/898/11339/4288/9134/2237/9918/699/1063/26271/55055/54892/79980/9735/23310/292/10051/1104/5359/83990/5885/2072/84722/51115/7283/80010/51647/54908/10592/6732/54069
GO:0000819                                                                                                                                                                                                                                                                                                         55143/991/9493/1062/10403/7153/23397/9787/11065/51203/10460/4751/4085/81930/81620/7272/64151/9212/9319/9055/3833/146909/891/24137/9232/9928/11004/990/5347/29127/26255/701/11130/10615/79075/9700/2237/9918/699/1063/26271/55055/54892
GO:0000280                                                                          55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/51203/22974/10460/4751/10635/27338/4085/81930/81620/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790/891/24137/9232/9928/1164/11004/4603/990/5347/29127/26255/701/11130/10615/79075/8438/9700/5888/898/56992/4288/9134/2175/91646/994/9918/699/1063/26271/55055/54892/5902/79980/9585/9735/23310/2253/8877/9088/995/10051/79703/1104/79866/83990/5885/11200/2072/940/1761/84722/51115/7283/80010
GO:0000070                                                                                                                                                                                                                                                                                                                   55143/991/9493/1062/10403/23397/9787/11065/51203/10460/4751/4085/81930/81620/7272/64151/9212/9319/9055/3833/146909/891/24137/9232/9928/11004/990/5347/29127/26255/701/11130/10615/79075/9700/9918/699/1063/26271/55055/54892
GO:0051301 55143/991/9493/1062/9133/10403/7153/23397/79733/259266/55165/11065/220134/51203/83461/22974/10460/4751/27338/890/983/54821/4085/5080/81620/332/3832/64151/9212/9055/3833/146909/10112/6790/891/24137/9232/9928/1164/11004/993/990/5347/29127/701/11130/57405/10615/1894/9700/898/23594/11339/3070/10733/1163/54801/9134/29899/54962/994/9918/1058/54478/699/4609/1063/26271/55055/641/8872/5898/3925/54892/4904/29901/8317/79980/9585/9735/10907/2810/23310/5499/2253/55726/8607/995/10051/1104/84790/1019/79866/83990/5885/11200/10263/203068
GO:0098813                                                                                                                                                                                                                                                                                                 55143/991/9493/1062/10403/7153/23397/9787/11065/51203/10460/4751/4085/81930/81620/7272/64151/9212/9319/9055/3833/146909/891/24137/9232/9928/11004/990/5347/29127/26255/701/11130/10615/1894/79075/9700/898/9134/2237/9918/699/1063/26271/55055
> 
> # Using three random descriptions
> dotplot(out.test,
+    showCategory=c("chromosome separation", "respiratory tube development", "metaphase/anaphase transition of cell cycle")  )
> 
> 
> 

enter image description here

ADD COMMENT

Login before adding your answer.

Traffic: 502 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6