Warning when making dotplot from gseaResult

[millerh1]

Hello! This has only been occurring recently -- but dotplot throws a strange warning when applied to objects of 'gseaResult' ---

wrong orderBy parameter; set to default orderBy = "x"

orderBy appears to be an internal parameter, so it's a bit confusing to get this error when it doesn't appear that there was an obvious way to set 'orderBy' in the first place.

Anyways -- also wanted to say I love the clusterProfiler/enrichPlot suite of tools, thank you for all the work your team does!! Hope this helps!

Reproducible example:

Quiescent.vs.Proliferative.Raw.Counts.txt

# Wrangle count data
counts <- read.table("Data/Quiescent.vs.Proliferative.Raw.Counts.txt", header = T, row.names = 1)
colData <- data.frame(sample = colnames(counts), condition = c(rep("Quiescent", 3), rep("Proliferative", 3)))
colData$condition <- factor(colData$condition, levels = c("Quiescent", "Proliferative"))
dds <- DESeqDataSetFromMatrix(countData = counts, colData = colData, design = ~condition)

# QC
keep <- rowSums(counts(dds)) >= 10
dds <- dds[keep,]

# DGE
dds <- DESeq(dds)
res <- results(dds, contrast = c("condition", "Quiescent", "Proliferative"))
resDF <- as.data.frame(res)
resDF$geneID <- rownames(resDF)

# wrange DGE results
ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl", host = "useast.ensembl.org") 
map <- getBM(attributes = c("ensembl_gene_id", "description", "external_gene_name"), mart = ensembl)
colnames(map) <- c("geneID", "description", "geneName")
resDF <- merge(x = map, y = resDF, by = "geneID")
resDF <- resDF[,c(3,2,1,4:9)]
resDF$GSEA <- -log10(resDF$padj) * sign(resDF$log2FoldChange)
resDF <- resDF[order(resDF$GSEA, decreasing = T),]

# GSEA
geneList <- resDF$GSEA
names(geneList) <- resDF$geneName
geneList <- geneList[which(! duplicated(names(geneList)))]
geneList <- geneList[which(! is.na(geneList))]
TERM2GENE <- msigdbr()
TERM2GENE <- TERM2GENE[,c(1,5)]
EGMT <- GSEA(geneList = geneList, TERM2GENE = TERM2GENE, pvalueCutoff = .2)

enrichplot::dotplot(EGMT)`

wrong orderBy parameter; set to default orderBy = "x"

Session info:

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] pheatmap_1.0.12             biomaRt_2.40.0              msigdbr_6.2.1               tibble_2.1.1               
 [5] dplyr_0.8.1                 EnhancedVolcano_1.2.0       ggrepel_0.8.1               ggplot2_3.1.1              
 [9] clusterProfiler_3.12.0      DESeq2_1.24.0               SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
[13] BiocParallel_1.18.0         matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0       
[17] GenomeInfoDb_1.20.0         IRanges_2.18.0              S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
  [1] fgsea_1.10.0           colorspace_1.4-1       ggridges_0.5.1         qvalue_2.16.0          htmlTable_1.13.1      
  [6] XVector_0.24.0         base64enc_0.1-3        rstudioapi_0.10        farver_1.1.0           urltools_1.7.3        
 [11] bit64_0.9-7            AnnotationDbi_1.46.0   xml2_1.2.0             splines_3.6.0          GOSemSim_2.10.0       
 [16] geneplotter_1.62.0     knitr_1.23             polyclip_1.10-0        Formula_1.2-3          jsonlite_1.6          
 [21] SMVar_1.3.3            packrat_0.5.0          annotate_1.62.0        cluster_2.0.8          GO.db_3.8.2           
 [26] ggforce_0.2.2          BiocManager_1.30.4     compiler_3.6.0         httr_1.4.0             rvcheck_0.1.3         
 [31] backports_1.1.4        assertthat_0.2.1       Matrix_1.2-17          lazyeval_0.2.2         limma_3.40.2          
 [36] tweenr_1.0.1           acepack_1.4.1          htmltools_0.3.6        prettyunits_1.0.2      tools_3.6.0           
 [41] igraph_1.2.4.1         gtable_0.3.0           glue_1.3.1             GenomeInfoDbData_1.2.1 reshape2_1.4.3        
 [46] DO.db_2.9              fastmatch_1.1-0        Rcpp_1.0.1             enrichplot_1.4.0       gdata_2.18.0          
 [51] ggraph_1.0.2           xfun_0.7               stringr_1.4.0          gtools_3.8.1           XML_3.98-1.19         
 [56] DOSE_3.10.0            europepmc_0.3          zlibbioc_1.30.0        MASS_7.3-51.4          scales_1.0.0          
 [61] hms_0.4.2              RColorBrewer_1.1-2     curl_3.3               memoise_1.1.0          gridExtra_2.3         
 [66] UpSetR_1.4.0           triebeard_0.3.0        rpart_4.1-15           metaMA_3.1.2           latticeExtra_0.6-28   
 [71] stringi_1.4.3          RSQLite_2.1.1          genefilter_1.66.0      checkmate_1.9.3        caTools_1.17.1.2      
 [76] rlang_0.3.4            pkgconfig_2.0.2        bitops_1.0-6           lattice_0.20-38        purrr_0.3.2           
 [81] labeling_0.3           htmlwidgets_1.3        cowplot_0.9.4          bit_1.1-14             tidyselect_0.2.5      
 [86] plyr_1.8.4             magrittr_1.5           R6_2.4.0               gplots_3.0.1.1         Hmisc_4.2-0           
 [91] DBI_1.0.0              withr_2.1.2            pillar_1.4.0           foreign_0.8-71         survival_2.44-1.1     
 [96] RCurl_1.95-4.12        nnet_7.3-12            crayon_1.3.4           KernSmooth_2.23-15     viridis_0.5.1         
[101] progress_1.2.2         locfit_1.5-9.1         grid_3.6.0             data.table_1.12.2      blob_1.1.1            
[106] digest_0.6.19          xtable_1.8-4           tidyr_0.8.3            gridGraphics_0.4-1     munsell_0.5.0         
[111] viridisLite_0.3.0      ggplotify_0.0.3   

[GuangchuangYu]

it should be fixed in recent version.

[zhaoqingbo1993]

Has this problem been solved?

[zhaoqingbo1993]

So it is fixed now? How can i adjust myplot?

[bounlu]

How is this solved? I still get this warning.

[jihoonk1495]

@bounlu I am also getting the same error when I am running dotplot.

I am following the vignette posted on this link:
https://learn.gencore.bio.nyu.edu/rna-seq-analysis/gene-set-enrichment-analysis/

[BirongZhang]

I am also getting the same error, how can we solve it?

ego <- enrichGO(gene = sig_genes,
universe = all_genes,
keyType = "ENSEMBL",
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
qvalueCutoff = 0.05,
readable = TRUE)

dotplot(ego, showCategory=50)

[hreinwal]

Same here :/ Still getting the same error.

[bounlu]

Has this problem been solved?

no

[huerqiang]

Please use the latest version on github.

[ChristinaSchmidt1]

I am using the latest version and yet I still get this warning.
Any other advice on how to solve this?

[ge2sasag]

Same, I'm still getting this all the time.

[OliverBit]

Same

[alexandruioanvoda]

I'm using the 1.10.2 version, latest, and I'm still getting this error all the time.

[MWSchmid]

Got the same error, but one can also just set the argument...

dotplot(myResults, showCategory=15, orderBy="GeneRatio")

[huerqiang]

@alexandruioanvoda the latest version of enrichplot in github is 1.11.3

[nat-kreiling]

I must be looking in the wrong place because The latest version in GitHub says 1.10.1 (https://github.com/YuLab-SMU/enrichplot) ?
I still tried updating enrichplot and am still getting this error: (even if I try specifying the orderBy argument)

barplot(ego_BP_up, 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

Update:
Trying the Devel version 1.11.3 still gives the same error. 😪

[huerqiang]

@nat-kreiling The class of your ego_BP_up should be enrichResult.

[shanshenbing]

I use 1.15.3, and the res from enrichKEGG() is "enrichResult" obj, but I got the same warning

[huerqiang]

I use 1.15.3, and the res from enrichKEGG() is "enrichResult" obj, but I got the same warning

Please provide your data.