ridgeplot doesn't work: Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero
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Y.K • 0
@62355d8e
Last seen 4 months ago
Japan

I am doing a GSEA analysis with clusterprofiler, but I am getting an error in ridgeplot. This is my code. I get an error even if I set pvalueCutoff to 1. How can I solve the problem? Thanks.

,,,df = read.csv("T00.csv", header=TRUE) ,,,original_gene_list_0_2 <- df_0$logFC ,,,names(original_gene_list_0_2) <- df_0$X ,,,head(original_gene_list_0_2) ,,,gene_list_0_2<-na.omit(original_gene_list_0_2) ,,,gene_list_0_2 = sort(gene_list_0_2, decreasing = TRUE) ,,,gsebp_0_2 <- gseGO(geneList=gene_list_0_2, ont="BP", keyType = "SYMBOL",
minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, nPermSimple = 10000, OrgDb =org.Hs.eg.db, pAdjustMethod = "none") ,,,ridgeplot(gsebp_0_2,showCategory = 8)

,,,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 enter image description here

sessionInfo( )

setting value version R version 4.2.1 (2022-06-23) os macOS Monterey 12.4 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Asia/Tokyo date 2022-07-22 rstudio 2022.07.0+548 Spotted Wakerobin (desktop) pandoc NA

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1 /Library/Frameworks/R.framework/Versions/4.2/Resources/library

clusterProfiler • 866 views
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Hi Y.k, have you solved your problem? I have same error.

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Because of lack of formatting, the post of the TS is difficult to read. Combined with the unavailability of the input data that was used, this question was not answered.

Having said this, the code works in my hands!

Since the input data was unavailable, I used as input the example dataset included with the library DOSE. Moreover, I included the argument eps=0. All other arguments are the same as used by the TS.

So I suggest you first check whether the code below runs for you as well. If not, be sure to update to the latest version of all libraries. If it does, then continue with your input data. If you then run into problems, fee free to post here (with sufficient details!).

> library(clusterProfiler)
> library(org.Hs.eg.db)
>   
> data(geneList, package="DOSE") ## use example data (for reproducibility)
>  
> gsebp <- gseGO(geneList=geneList,
+   ont="BP",
+   keyType = "ENTREZID",
+   minGSSize = 3,
+   maxGSSize = 800,
+   pvalueCutoff = 0.05,
+   verbose = TRUE,
+   nPermSimple = 10000,
+   eps = 0,
+   OrgDb =org.Hs.eg.db,
+   pAdjustMethod = "none")
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
> 
> 
> 
> ridgeplot(gsebp,showCategory = 8)
Picking joint bandwidth of 0.284
> 

enter image description here

> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] org.Hs.eg.db_3.15.0   AnnotationDbi_1.58.0  IRanges_2.30.1       
[4] S4Vectors_0.34.0      Biobase_2.56.0        BiocGenerics_0.42.0  
[7] clusterProfiler_4.4.4

loaded via a namespace (and not attached):
  [1] nlme_3.1-159           bitops_1.0-7           ggtree_3.4.4          
  [4] enrichplot_1.16.2      bit64_4.0.5            RColorBrewer_1.1-3    
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I had the same problem, which was solved when I used "EMSEMBL" or "ENTREZID" for keyType matching. I guess some duplicated SYMBOLs in our data may cause the issue.

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