Entering edit mode
13 months ago
Victor
•
0
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
Please edit your post and add the output to
sessionInfo().Hi Ram, I have edited the post. Thank you for your consideration.
Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), 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.