Hello

I used this code to do a GO enrchment analisis with topGO as im working with Hydractinia symbiolongicarpus but i get this error when trying to use enrichplot to made a dotplot, anyone have any idea on how to fix it? or any idea of other packages to use?

library(topGO)
library(dplyr)
library(enrichplot)

all_genes <- genelist$gene_id
interesting_genes <- cluster_go$gene_id
geneList <- factor(as.integer (all_genes %in% interesting_genes))
geneList
names (geneList) <- all_genes
GO2genes <- cluster_GO %>% 
     group_by(GO) %>%
     summarize(genes = list(unique(gene_id))) %>%
     with(setNames(genes, GO))
GOdata <- new("topGOdata",
               ontology = "BP",
               allGenes = geneList,
               nodeSize = 5,
               annot = annFUN.GO2genes,
               GO2genes = GO2genes)
result <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
dot <- GenTable(GOdata, classicFisher = result, topNodes = 10)
dot
        GO.ID                                        Term Annotated Significant Expected
1  GO:0000003                                reproduction        89          89       89
2  GO:0000041              transition metal ion transport         7           7        7
3  GO:0000045                      autophagosome assembly         8           8        8
4  GO:0000070        mitotic sister chromatid segregation         9           9        9
5  GO:0000075             cell cycle checkpoint signaling        11          11       11
6  GO:0000077             DNA damage checkpoint signaling         8           8        8
7  GO:0000082       G1/S transition of mitotic cell cycle         8           8        8
8  GO:0000086       G2/M transition of mitotic cell cycle        12          12       12
9  GO:0000122 negative regulation of transcription by ...        20          20       20
10 GO:0000165                                MAPK cascade        25          25       25
   classicFisher
1              1
2              1
3              1
4              1
5              1
6              1
7              1
8              1
9              1
10             1

You need to get familiar with the help system for R. There is a help page for dotplot which indicates what sort of input dotplot expects (not a data.frame), and also has an example that you can emulate. There is also an actual book that you could read.

The enrichplot package doesn't depend on (or suggest) topGO, so there is no reason that you should expect that the output from topGO should be suitable as input to functions in enrichplot.