guidohooiveld
commented
1 year ago You did not provide your input data, but I suspect this is due to the fact that you use gene symbols as input. From my experience gene symbols are regularly duplicated (= the same gene symbol is used for 2 different genes; see below for examples), and as a result the ridgeplot fails (because that plots all genes belonging to a gene set). The dotplot will work because that plots only the results from the gene sets as such; no info on constituent genes is needed for such plot.
I suggest you use unique identifiers in all your analyses, such as entrez or ensembl ids.
>
> library(org.Hs.eg.db)
> ids <- keys(org.Hs.eg.db)
>
> mapping <- select(org.Hs.eg.db, keys=ids, columns=c('ENTREZID','SYMBOL'), keytype='ENTREZID')
'select()' returned 1:1 mapping between keys and columns
> mapping[duplicated(mapping[,"SYMBOL"]),]
ENTREZID SYMBOL
4795 6052 RNR1
4796 6053 RNR2
11493 51072 MEMO1
28771 100124696 TEC
30812 100187828 HBD
35761 100505381 MMD2
53263 107648861 DEL11P13
54541 107985615 TRNAV-CAC
54642 107985753 TRNAV-CAC
63864 122405565 SMIM44
64999 123670537 DEL1P36
>
> select(org.Hs.eg.db, keys="HBD", columns=c('ENTREZID','SYMBOL'), keytype='SYMBOL')
'select()' returned 1:many mapping between keys and columns
SYMBOL ENTREZID
1 HBD 3045
2 HBD 100187828
>
>
> select(org.Hs.eg.db, keys="MEMO1", columns=c('ENTREZID','SYMBOL'), keytype='SYMBOL')
'select()' returned 1:many mapping between keys and columns
SYMBOL ENTREZID
1 MEMO1 7795
2 MEMO1 51072
>
>
> select(org.Hs.eg.db, keys="TRNAV-CAC", columns=c('ENTREZID','SYMBOL'), keytype='SYMBOL')
'select()' returned 1:many mapping between keys and columns
SYMBOL ENTREZID
1 TRNAV-CAC 107985614
2 TRNAV-CAC 107985615
3 TRNAV-CAC 107985753
>
```> 
mick42-star
javifar
I use ‘clusterProfiler’ version 4.5.1.902 to do gse analysis, I got gse result and related dotplot, however, I cannot generate ridgeplot.
gse <- gseGO(geneList=gene_list, ont ="ALL", keyType = "SYMBOL", nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = "org.Mm.eg.db", pAdjustMethod = "none")
dotplot(gse, showCategory=10, split=".sign") + facet_grid(.~.sign)
ridgeplot(gse)
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero