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WGCNA plotEigengeneNetworks error (coercion to logical)

Hi everyone, hope you are all well.

I am trying to run the plotEigengeneNetworks function, however I am getting an error. I have used the same code for some time now but now I am using a new machine and another R version. The code and the error is as follows:

pdf(paste('5-eigengenesnetworks.pdf', sep=""),width = 20,height = 18)
colorBWR<-blueWhiteRed(50, gamma=3)
cex=0.2
plotEigengeneNetworks(multiME,setLabels=setLabels, letterSubPlots=T, plotDendrograms=T, 
                       marDendro=c(1,3,1.2,2), marHeatmap=c(2,3,2.5,5), excludeGrey=T, 
                      colorLabels=T, signed=F, setMargins=F, plotAdjacency=T, printAdjacency=T, 
                      heatmapColors=colorBWR, printPreservation=T)
Error in sum((1 - abs(dispd)) < zlimPreservation[1]) || ((1 - abs(dispd)) >  : 
  'length = 225' in coercion to 'logical(1)'

I would like to provide more information, but I really don't know where to begin to describe the error better. Here is the version records:

  • R version 4.3.1 (2023-06-16)
  • Platform: x86_64-pc-linux-gnu (64-bit)
  • Running under: Ubuntu 22.04.3 LTS

EDIT: sessionInfo() output

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Sao_Paulo
tzcode source: system (glibc)

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

other attached packages:
 [1] DESeq2_1.40.2               SummarizedExperiment_1.30.2 MatrixGenerics_1.12.3      
 [4] GenomicRanges_1.52.0        GenomeInfoDb_1.36.3         tximport_1.28.0            
 [7] lubridate_1.9.3             forcats_1.0.0               stringr_1.5.0              
[10] dplyr_1.1.3                 purrr_1.0.2                 readr_2.1.4                
[13] tidyr_1.3.0                 tibble_3.2.1                ggplot2_3.4.2              
[16] tidyverse_2.0.0             venn_1.11                   scales_1.2.1               
[19] UpSetR_1.4.0                DOSE_3.26.1                 org.Hs.eg.db_3.17.0        
[22] ReactomePA_1.44.0           enrichplot_1.20.3           clusterProfiler_4.8.3      
[25] igraph_1.5.1                gridExtra_2.3               latticeExtra_0.6-30        
[28] lattice_0.21-8              flashClust_1.01-2           robust_0.7-2               
[31] fit.models_0.64             Rcpp_1.0.11                 GO.db_3.17.0               
[34] AnnotationDbi_1.62.2        IRanges_2.34.1              S4Vectors_0.38.2           
[37] Biobase_2.60.0              BiocGenerics_0.46.0         preprocessCore_1.62.1      
[40] survival_3.5-5              doParallel_1.0.17           iterators_1.0.14           
[43] foreach_1.5.2               impute_1.74.1               Hmisc_5.1-1                
[46] matrixStats_1.0.0           WGCNA_1.72-1                fastcluster_1.2.3          
[49] dynamicTreeCut_1.63-1      

loaded via a namespace (and not attached):
  [1] bitops_1.0-7            ggplotify_0.1.2         polyclip_1.10-6        
  [4] graph_1.78.0            rpart_4.1.19            lifecycle_1.0.3        
  [7] MASS_7.3-60             backports_1.4.1         magrittr_2.0.3         
 [10] rmarkdown_2.25          yaml_2.3.7              cowplot_1.1.1          
 [13] DBI_1.1.3               RColorBrewer_1.1-3      abind_1.4-5            
 [16] zlibbioc_1.46.0         ggraph_2.1.0            RCurl_1.98-1.12        
 [19] yulab.utils_0.1.0       nnet_7.3-19             rappdirs_0.3.3         
 [22] tweenr_2.0.2            GenomeInfoDbData_1.2.10 ggrepel_0.9.3          
 [25] tidytree_0.4.5          reactome.db_1.84.0      codetools_0.2-19       
 [28] DelayedArray_0.26.7     ggforce_0.4.1           tidyselect_1.2.0       
 [31] aplot_0.2.1             farver_2.1.1            viridis_0.6.4          
 [34] base64enc_0.1-3         jsonlite_1.8.7          tidygraph_1.2.3        
 [37] Formula_1.2-5           tools_4.3.1             treeio_1.24.3          
 [40] glue_1.6.2              admisc_0.33             xfun_0.40              
 [43] qvalue_2.32.0           withr_2.5.0             fastmap_1.1.1          
 [46] fansi_1.0.4             digest_0.6.33           timechange_0.2.0       
 [49] R6_2.5.1                gridGraphics_0.5-1      colorspace_2.1-0       
 [52] jpeg_0.1-10             RSQLite_2.3.1           utf8_1.2.3             
 [55] generics_0.1.3          data.table_1.14.8       robustbase_0.99-0      
 [58] graphlayouts_1.0.1      httr_1.4.7              htmlwidgets_1.6.2      
 [61] S4Arrays_1.0.6          scatterpie_0.2.1        graphite_1.46.0        
 [64] pkgconfig_2.0.3         gtable_0.3.3            blob_1.2.4             
 [67] XVector_0.40.0          pcaPP_2.0-3             shadowtext_0.1.2       
 [70] htmltools_0.5.6         fgsea_1.26.0            png_0.1-8              
 [73] ggfun_0.1.3             knitr_1.44              rstudioapi_0.15.0      
 [76] tzdb_0.4.0              reshape2_1.4.4          checkmate_2.2.0        
 [79] nlme_3.1-162            cachem_1.0.8            HDO.db_0.99.1          
 [82] foreign_0.8-82          pillar_1.9.0            vctrs_0.6.3            
 [85] cluster_2.1.4           htmlTable_2.4.1         evaluate_0.22          
 [88] mvtnorm_1.2-3           cli_3.6.1               locfit_1.5-9.8         
 [91] compiler_4.3.1          rlang_1.1.1             crayon_1.5.2           
 [94] rrcov_1.7-4             interp_1.1-4            plyr_1.8.9             
 [97] fs_1.6.3                stringi_1.7.12          viridisLite_0.4.2      
[100] deldir_1.0-9            BiocParallel_1.34.2     munsell_0.5.0          
[103] Biostrings_2.68.1       lazyeval_0.2.2          GOSemSim_2.26.1        
[106] Matrix_1.6-0            hms_1.1.3               patchwork_1.1.3        
[109] bit64_4.0.5             KEGGREST_1.40.1         memoise_2.0.1          
[112] ggtree_3.8.2            fastmatch_1.1-4         DEoptimR_1.1-2         
[115] bit_4.0.5               downloader_0.4          ape_5.7-1              
[118] gson_0.1.0

Thank you in advance

wgcna ploteigengenenetworks rna-seq rstudio
• 1,322 views • link
updated by Ram Ram • written by Victor • Victor

Please edit your post and add the output to sessionInfo().

• 0 views • link
written by Ram Ram

Hi Ram, I have edited the post. Thank you for your consideration.

• 0 views • link
written by Victor • Victor

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.
code_formatting

• 0 views • link
written by Ram Ram

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