Dotplot and barplot shows (Error in ans[ypos] <- rep(yes, length.out = len)[ypos] ) and a warning message, even though the enrichResult is not emplty

[Chanukya-Pavan]

I ran the general pipeline with entrez_ids from my DEG analysis

gene_list <- DEG_genes_WT1_cells_myo %>% filter(avg_log2FC >= 0.4) %>% pull(X)

entrez_ids <- bitr(gene_list, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)$ENTREZID

kegg_results <- enrichKEGG(entrez_ids, organism = "hsa", keyType = "kegg", pvalueCutoff = 0.05, pAdjustMethod = "BH", minGSSize = 5, use_internal_data = F)

kegg_results <- setReadable(kegg_results, OrgDb = org.Hs.eg.db, keyType = "ENTREZID")

when I ran for visualization, the following error were shown

> dotplot(kegg_results, showCategory = 20)
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
  replacement has length zero
In addition: Warning message:
In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL
> barplot(kegg_results, showCategory = 5)
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
  replacement has length zero
In addition: Warning message:
In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL

the following libraries were called out

library(clusterProfiler)
library(org.Hs.eg.db)
library(dplyr)
library(DOSE)
library(enrichplot)

every one of them is up-to-date

enrichplot_1.26.6      DOSE_4.0.0             org.Hs.eg.db_3.20.0    AnnotationDbi_1.68.0   IRanges_2.40.1         S4Vectors_0.44.0       Biobase_2.66.0        
 [8] BiocGenerics_0.52.0    clusterProfiler_4.14.4 RColorBrewer_1.1-3     DoubletFinder_2.0.4    harmony_1.2.3          Rcpp_1.0.14            gridExtra_2.3         
[15] RCurl_1.98-1.16        lubridate_1.9.4        forcats_1.0.0          stringr_1.5.1          purrr_1.0.4            readr_2.1.5            tidyr_1.3.1           
[22] tibble_3.2.1           ggplot2_3.5.1          tidyverse_2.0.0        dplyr_1.1.4            patchwork_1.3.0        cowplot_1.1.3          Seurat_5.2.1          
[29] SeuratObject_5.0.2     sp_2.2-0  

Please let me know what to do as I looked at multiple places and haven't found anything yet. Thanks in advance

Chanukya

[guidohooiveld]

Are you sure there are gene sets to be visualized?

In other words, what is the output from kegg_results and as.data.frame(kegg_results)[1:5,]?

Also, for testing, what happens if you set the argument pvalueCutoff = 1 (no cutoff is then being applied, so there should be results).