YuLab-SMU
goplot does not find ontology
Hi, I am trying to reproduce the example code provided below and i get an error
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
> head(yy)
ID Description GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
GO:0007059 GO:0007059 chromosome segregation 34/99 431/18805 0.07888631 14.98441 21.36650 4.744689e-31
GO:0098813 GO:0098813 nuclear chromosome segregation 31/99 322/18805 0.09627329 18.28706 22.76225 6.561567e-31
GO:0000819 GO:0000819 sister chromatid segregation 28/99 234/18805 0.11965812 22.72900 24.33225 1.457950e-30
GO:0000070 GO:0000070 mitotic sister chromatid segregation 26/99 193/18805 0.13471503 25.58905 24.97906 9.463712e-30
GO:0140014 GO:0140014 mitotic nuclear division 29/99 282/18805 0.10283688 19.53381 22.81319 1.026099e-29
GO:0000280 GO:0000280 nuclear division 33/99 448/18805 0.07366071 13.99182 20.24698 3.996836e-29
p.adjust qvalue
GO:0007059 5.367362e-28 4.306460e-28
GO:0098813 5.367362e-28 4.306460e-28
GO:0000819 7.950689e-28 6.379172e-28
GO:0000070 3.357397e-27 2.693781e-27
GO:0140014 3.357397e-27 2.693781e-27
GO:0000280 1.089804e-26 8.743954e-27
geneID
GO:0007059 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/55355/220134/51203/22974/10460/4751/79019/55839/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909/6790
GO:0098813 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909/6790
GO:0000819 55143/991/9493/1062/4605/10403/7153/23397/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909
GO:0000070 55143/991/9493/1062/4605/10403/23397/9787/11065/220134/51203/22974/4751/983/4085/81930/81620/332/3832/7272/64151/9212/9319/9055/3833/146909
GO:0140014 55143/991/9493/1062/4605/10403/23397/9787/11065/220134/51203/22974/4751/27338/983/4085/81930/81620/332/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790
GO:0000280 55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/220134/51203/22974/4751/10635/27338/983/4085/81930/81620/332/3832/7272/64151/9212/1111/9319/9055/3833/146909/6790
Count
GO:0007059 34
GO:0098813 31
GO:0000819 28
GO:0000070 26
GO:0140014 29
GO:0000280 33
This is the error, the object contains the ontology so dont know the problem ?
> goplot(yy)
Error in goplot.enrichResult(x, showCategory = showCategory, color = color, :
Ontology should be one of 'MF', 'CC' or 'BP'
> yy@ontology
[1] "BP"
Subset of the returned yy object:
> str(yy)
Formal class 'enrichResult' [package "DOSE"] with 15 slots
..@ result :'data.frame': 1636 obs. of 12 variables:
.. ..$ ID : chr [1:1636] "GO:0007059" "GO:0098813" "GO:0000819" "GO:0000070" ...
.. ..$ Description : chr [1:1636] "chromosome segregation" "nuclear chromosome segregation" "sister chromatid segregation" "mitotic sister chromatid segregation" ...
.. ..$ GeneRatio : chr [1:1636] "34/99" "31/99" "28/99" "26/99" ...
.. ..$ BgRatio : chr [1:1636] "431/18805" "322/18805" "234/18805" "193/18805" ...
.. ..$ RichFactor : num [1:1636] 0.0789 0.0963 0.1197 0.1347 0.1028 ...
.. ..$ FoldEnrichment: num [1:1636] 15 18.3 22.7 25.6 19.5 ...
.. ..$ zScore : num [1:1636] 21.4 22.8 24.3 25 22.8 ...
.. ..$ pvalue : num [1:1636] 4.74e-31 6.56e-31 1.46e-30 9.46e-30 1.03e-29 ...
.. ..$ p.adjust : num [1:1636] 5.37e-28 5.37e-28 7.95e-28 3.36e-27 3.36e-27 ...
.. ..$ qvalue : num [1:1636] 4.31e-28 4.31e-28 6.38e-28 2.69e-27 2.69e-27 ...
.. ..$ geneID : chr [1:1636] "55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/55355/220134/51203/22974/10460/4751/79019/5583"| __truncated__ "55143/991/9493/1062/4605/9133/10403/7153/23397/259266/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/8"| __truncated__ "55143/991/9493/1062/4605/10403/7153/23397/9787/11065/220134/51203/22974/10460/4751/983/4085/81930/81620/332/383"| __truncated__ "55143/991/9493/1062/4605/10403/23397/9787/11065/220134/51203/22974/4751/983/4085/81930/81620/332/3832/7272/6415"| __truncated__ ...
.. ..$ Count : int [1:1636] 34 31 28 26 29 33 33 21 20 17 ...
..@ pvalueCutoff : num 0.01
..@ pAdjustMethod: chr "BH"
..@ qvalueCutoff : num 0.2
..@ organism : chr "Homo sapiens"
..@ ontology : chr "BP"
..@ gene : chr [1:100] "4312" "8318" "10874" "55143" ...
..@ keytype : chr "ENTREZID"
..@ universe : chr [1:18805] "142" "291" "1763" "1890" ...
..@ gene2Symbol : chr(0)
..@ geneSets :List of 2248
.. ..$ GO:0000018: chr [1:142] "25" "60" "86" "142" ...
.. ..$ GO:0000022: chr [1:12] "332" "3619" "4926" "6795" ...
.. ..$ GO:0000070: chr [1:193] "324" "332" "387" "472" ...
...
.. .. [list output truncated]
..@ readable : logi FALSE
..@ termsim : num[0 , 0 ]
..@ method : chr(0)
..@ dr : list()
>
Running the packages below for clusterProfiler and R
packageVersion("clusterProfiler") [1] ‘4.16.0’ R.version _
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 5.0
year 2025
month 04
day 11
svn rev 88135
language R
version.string R version 4.5.0 (2025-04-11) nickname How About a Twenty-Six
Any idea of what is wrong ???
I am getting excactly the same error from goplot() in any type of enrich result object I have tried
My clusterProfiler and R details as follows:
packageVersion("clusterProfiler") [1] ‘4.16.0’ R.version _
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 5.0
year 2025
month 04
day 11
svn rev 88135
language R
version.string R version 4.5.0 (2025-04-11) nickname How About a Twenty-Six
I have the same problem, there's a bug in the goplot function which is provided by the enrichplot package. In goplot, the recently introduced ontology check where it checks for BF instead of BP, this line specifically. It's a quick fix, I submitted a pull request here: https://github.com/YuLab-SMU/enrichplot/pull/321
In the meantime, the fork works well:
devtools::install_github("davorvr/enrichplot")
library(enrichplot)
library(clusterProfiler)
