emapplot with Error in `geom_edge_link()`

[PeterWang0502]

Hi, I'm testing code in your web tutorial here: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html, and I ran into some error. When I try to make emapplot with parameter showCategory of less than or equal to 4, everything is fine. But for any higher value, it would report the following error:

Error in geom_edge_link():
! Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in pathAttr():
! 'names' attribute [6141255744] must be the same length as the vector [2]
Run rlang::last_trace() to see where the error occurred.

Below is my code:

library(ggplot2)
library(enrichplot)
library(DOSE)
data(geneList)
de <- names(geneList)[abs(geneList) > 2]
edo <- enrichDGN(de)
edo <- pairwise_termsim(edo)
p1 <- emapplot(edo, showCategory=5, cex.params=list(category_label=0.5))
p1

And below is my R session information:

R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Monterey 12.5.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] DOSE_3.30.5 enrichplot_1.24.4 ggplot2_3.5.1

loaded via a namespace (and not attached):
[1] DBI_1.2.3 shadowtext_0.1.4 gridExtra_2.3 httr2_1.1.0
[5] rlang_1.1.5 magrittr_2.0.3 compiler_4.4.1 RSQLite_2.3.9
[9] png_0.1-8 vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1
[13] pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0 XVector_0.44.0
[17] labeling_0.4.3 ggraph_2.2.1 UCSC.utils_1.0.0 purrr_1.0.2
[21] bit_4.5.0.1 zlibbioc_1.50.0 cachem_1.1.0 aplot_0.2.4
[25] GenomeInfoDb_1.40.1 jsonlite_1.8.9 blob_1.2.4 BiocParallel_1.38.0
[29] tweenr_2.0.3 parallel_4.4.1 R6_2.5.1 stringi_1.8.4
[33] RColorBrewer_1.1-3 GOSemSim_2.30.2 Rcpp_1.0.14 R.utils_2.12.3
[37] IRanges_2.38.1 Matrix_1.7-2 splines_4.4.1 igraph_2.1.4
[41] tidyselect_1.2.1 qvalue_2.36.0 viridis_0.6.5 codetools_0.2-20
[45] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9 Biobase_2.64.0
[49] treeio_1.28.0 withr_3.0.2 KEGGREST_1.44.1 gridGraphics_0.5-1
[53] scatterpie_0.2.4 polyclip_1.10-7 Biostrings_2.72.1 pillar_1.10.1
[57] ggtree_3.12.0 stats4_4.4.1 ggfun_0.1.8 generics_0.1.3
[61] S4Vectors_0.42.1 munsell_0.5.1 scales_1.3.0 tidytree_0.4.6
[65] glue_1.8.0 lazyeval_0.2.2 tools_4.4.1 ggnewscale_0.5.0
[69] data.table_1.16.4 fgsea_1.30.0 fs_1.6.5 graphlayouts_1.2.2
[73] fastmatch_1.1-6 tidygraph_1.3.1 cowplot_1.1.3 grid_4.4.1
[77] tidyr_1.3.1 ape_5.8-1 AnnotationDbi_1.66.0 colorspace_2.1-1
[81] nlme_3.1-167 GenomeInfoDbData_1.2.12 patchwork_1.3.0 ggforce_0.4.2
[85] cli_3.6.3 rappdirs_0.3.3 viridisLite_0.4.2 dplyr_1.1.4
[89] gtable_0.3.6 R.methodsS3_1.8.2 yulab.utils_0.2.0 digest_0.6.37
[93] BiocGenerics_0.50.0 ggrepel_0.9.6 ggplotify_0.1.2 farver_2.1.2
[97] memoise_2.0.1 R.oo_1.27.0 lifecycle_1.0.4 httr_1.4.7
[101] GO.db_3.19.1 bit64_4.6.0-1 MASS_7.3-64

Any help is appreciated. Thanks!

[guidohooiveld]

Note that I do not have the versions of R/Bioconductor installed anymore that you are using. It also not fully clear to me what you try to achieve... Based on your code I assume you would like to increase the size of the nodes.

Yet, when using the latest release version of enrichplot (i.e. 1.26.6) your code works, yet with a small modification. That is, since this release the functions emapplot (and cnetplot) have been completely rewritten (in order to allow more flexibility in fine-tuning the plots). As a consequence, some arguments have been modified as well. It turns out the code on the website has not been updated to reflect these changes.

Anyway, to increase or decrease the size of the nodes reflecting the DisGeNET gene sets, the argument size_category should be used (default: size_category = 1) instead of category_label. See ?emapplot for more info on all arguments.

> library(ggplot2)
> library(enrichplot)
>
> de <- names(geneList)[abs(geneList) > 2]
> edo <- enrichDGN(de)
> edo <- pairwise_termsim(edo)
> p1 <- emapplot(edo, showCategory=5, cex.params=list(category_label=0.5))
Error in emapplot_internal(x, showCategory = showCategory, ...) : 
  unused argument (cex.params = list(0.5))
>
> ## instead use argument 'size_category'
> p1 <- emapplot(edo, showCategory=5, size_category=1) ## default
>
> p2 <- emapplot(edo, showCategory=5, size_category=0.5)
>
> p3 <- emapplot(edo, showCategory=5, size_category=2)
> 
> packageVersion("enrichplot")
[1] ‘1.26.6’
> BiocManager::version()
[1] ‘3.20’
> 
> 
> print(p1)
> 
> print(p2)
> 
> print(p3)
> 

p1

p2

p3

[PeterWang0502]

Hi, after upgrading BiocManager and enrichplot to the latest release, I no longer have the errors. Thanks for your help!

[komalsrathi]

@PeterWang0502 @guidohooiveld Hi, I am facing exactly this issue. What version of R and Bioconductor are you using? My R version is 4.4.2 and enrichplot version is 1.24.4 and BiocVersion 3.19.

> packageVersion("BiocVersion")[,1:2]
[1] ‘3.19’

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] enrichplot_1.24.4           signatureSearch_1.18.0      org.Hs.eg.db_3.19.1         AnnotationDbi_1.65.2        SummarizedExperiment_1.34.0
 [6] Biobase_2.64.0              GenomicRanges_1.55.4        GenomeInfoDb_1.40.0         IRanges_2.38.0              S4Vectors_0.42.0           
[11] BiocGenerics_0.50.0         MatrixGenerics_1.16.0       matrixStats_1.5.0           Rcpp_1.0.14                 lubridate_1.9.4            
[16] forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.4                 readr_2.1.5                
[21] tidyr_1.3.1                 tibble_3.2.1                ggplot2_3.5.1               tidyverse_2.0.0            

[PeterWang0502]

@PeterWang0502 @guidohooiveld Hi, I am facing exactly this issue. What version of R and Bioconductor are you using? My R version is 4.4.2 and enrichplot version is 1.24.4 and BiocVersion 3.19.

> packageVersion("BiocVersion")[,1:2]
[1] ‘3.19’

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] enrichplot_1.24.4           signatureSearch_1.18.0      org.Hs.eg.db_3.19.1         AnnotationDbi_1.65.2        SummarizedExperiment_1.34.0
 [6] Biobase_2.64.0              GenomicRanges_1.55.4        GenomeInfoDb_1.40.0         IRanges_2.38.0              S4Vectors_0.42.0           
[11] BiocGenerics_0.50.0         MatrixGenerics_1.16.0       matrixStats_1.5.0           Rcpp_1.0.14                 lubridate_1.9.4            
[16] forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.4                 readr_2.1.5                
[21] tidyr_1.3.1                 tibble_3.2.1                ggplot2_3.5.1               tidyverse_2.0.0            

Hi, my R version is 4.4.1, and enrichplot version is 1.26.6 and BiocVersion is 3.20.0.

[guidohooiveld]

@komalsrathi

> packageVersion("enrichplot")
[1] ‘1.26.6’
> 
> BiocManager::version()
[1] ‘3.20’
> 
> R.Version()$version.string
[1] "R version 4.4.2 (2024-10-31 ucrt)"
> 

... in essence thus the same versions as @PeterWang0502