Error in 1:ncol(AllComb) : argument of length 0 when PlotPG()

[dnarna909]

I am running the basic codes for Elastic principal graph construction as showed in: https://rdrr.io/github/Albluca/ElPiGraph.R/f/guides/trim.Rmd

TreeEPG <- computeElasticPrincipalTree(X = TD_LowNoise, NumNodes = 40, drawAccuracyComplexity = FALSE, drawEnergy = FALSE, drawPCAView = FALSE, n.cores = 1)

But I keep getting error the run PlotPG function, as follow:

PlotPG(X = TD_LowNoise, TargetPG = TreeEPG[[1]], GroupsLab = TD_LowNoise_Cat, Do_PCA = FALSE, DimToPlot = 1:2)

Error in 1:ncol(AllComb) : argument of length 0

The TreeEPG file is generated. Any solutions for this issue?

This is my sessionInfo

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] en_US.UTF-8 attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] igraph_1.2.11 velocyto.R_0.6 gtsummary_1.5.2
[4] combinat_0.0-8 pander_0.6.4 ggpubr_0.4.0
[7] car_3.0-12 carData_3.0-5 venn_1.10
[10] RColorBrewer_1.1-2 readxl_1.3.1 EnsDb.Hsapiens.v86_2.99.0
[13] ensembldb_2.18.3 AnnotationFilter_1.18.0 GenomicFeatures_1.46.3
[16] org.Hs.eg.db_3.14.0 scDblFinder_1.9.4 seriation_1.3.1
[19] tradeSeq_1.8.0 monocle3_1.0.0 TSCAN_1.32.0
[22] slingshot_2.2.0 TrajectoryUtils_1.2.0 princurve_2.1.6
[25] ElPiGraph.R_1.0.0 phateR_1.0.7 glmnet_4.1-3
[28] edgeR_3.36.0 GEOquery_2.62.2 rWikiPathways_1.14.0
[31] clusterProfiler_4.2.2 dplyr_1.0.8 org.Mm.eg.db_3.14.0
[34] AnnotationDbi_1.56.2 lisi_1.0 kBET_0.99.6
[37] biomaRt_2.50.2 RANN_2.6.1 limma_3.50.0
[40] MAST_1.20.0 circlize_0.4.13 ComplexHeatmap_2.10.0
[43] harmony_0.1.0 Rcpp_1.0.8 batchelor_1.10.0
[46] DropletUtils_1.14.2 scater_1.22.0 ggplot2_3.3.5
[49] scran_1.22.1 scuttle_1.4.0 Matrix_1.4-0
[52] SeuratObject_4.0.4 Seurat_4.1.0 umap_0.2.7.0
[55] BiocSingular_1.10.0 simpleSingleCell_1.18.0 SingleCellExperiment_1.16.0 [58] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1
[61] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3
[64] BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
loaded via a namespace (and not attached): [1] graphlayouts_0.8.0 pbapply_1.5-0 lattice_0.20-45
[4] vctrs_0.3.8 fastICA_1.2-3 mgcv_1.8-38
[7] blob_1.2.2 survival_3.2-13 spatstat.data_2.1-2
[10] later_1.3.0 DBI_1.1.2 R.utils_2.11.0
[13] rappdirs_0.3.3 uwot_0.1.11 dqrng_0.3.0
[16] zlibbioc_1.40.0 pcaMethods_1.86.0 htmlwidgets_1.5.4
[19] GlobalOptions_0.1.2 future_1.23.0 leiden_0.3.9
[22] parallel_4.1.2 irlba_2.3.5 tidygraph_1.2.0
[25] readr_2.1.1 KernSmooth_2.23-20 promises_1.2.0.1
[28] DelayedArray_0.20.0 graph_1.72.0 RSpectra_0.16-0
[31] fastmatch_1.1-3 digest_0.6.29 png_0.1-7
[34] distutils_1.0 bluster_1.4.0 sctransform_0.3.3
[37] scatterpie_0.1.7 cowplot_1.1.1 DOSE_3.20.1
[40] here_1.0.1 ggraph_2.0.5 pkgconfig_2.0.3
[43] GO.db_3.14.0 DelayedMatrixStats_1.16.0 ggbeeswarm_0.6.0
[46] gt_0.3.1 iterators_1.0.13 reticulate_1.24
[49] beeswarm_0.4.0 GetoptLong_1.0.5 xfun_0.29
[52] zoo_1.8-9 tidyselect_1.1.1 reshape2_1.4.4
[55] purrr_0.3.4 ica_1.0-2 viridisLite_0.4.0
[58] rtracklayer_1.54.0 rlang_1.0.1 glue_1.6.1
[61] registry_0.5-1 stringr_1.4.0 tictoc_1.0.1
[64] ggsignif_0.6.3 httpuv_1.6.5 BiocNeighbors_1.12.0
[67] DO.db_2.9 jsonlite_1.7.3 XVector_0.34.0
[70] bit_4.0.4 mime_0.12 gridExtra_2.3
[73] gplots_3.1.1 Rsamtools_2.10.0 stringi_1.7.6
[76] processx_3.5.2 spatstat.sparse_2.1-0 scattermore_0.7
[79] yulab.utils_0.0.4 bitops_1.0-7 cli_3.1.1
[82] rhdf5filters_1.6.0 RSQLite_2.2.9 tidyr_1.2.0
[85] pheatmap_1.0.12 data.table_1.14.2 rstudioapi_0.13
[88] TSP_1.1-11 GenomicAlignments_1.30.0 nlme_3.1-155
[91] qvalue_2.26.0 locfit_1.5-9.4 listenv_0.8.0
[94] miniUI_0.1.1.1 gridGraphics_0.5-1 R.oo_1.24.0
[97] dbplyr_2.1.1 lifecycle_1.0.1 munsell_0.5.0
[100] cellranger_1.1.0 R.methodsS3_1.8.1 caTools_1.18.2
[103] codetools_0.2-18 vipor_0.4.5 lmtest_0.9-39
[106] admisc_0.23 xtable_1.8-4 ROCR_1.0-11
[109] abind_1.4-5 farver_2.1.0 FNN_1.1.3
[112] parallelly_1.30.0 ResidualMatrix_1.4.0 aplot_0.1.2
[115] askpass_1.1 ggtree_3.2.1 BiocIO_1.4.0
[118] RcppAnnoy_0.0.19 goftest_1.2-3 patchwork_1.1.1
[121] tibble_3.1.6 cluster_2.1.2 future.apply_1.8.1
[124] tidytree_0.3.7 ellipsis_0.3.2 prettyunits_1.1.1
[127] ggridges_0.5.3 mclust_5.4.9 fgsea_1.20.0
[130] spatstat.utils_2.3-0 htmltools_0.5.2 BiocFileCache_2.2.0
[133] yaml_2.2.2 utf8_1.2.2 plotly_4.10.0
[136] XML_3.99-0.8 withr_2.4.3 fitdistrplus_1.1-6
[139] CodeDepends_0.6.5 BiocParallel_1.28.3 bit64_4.0.5
[142] xgboost_1.5.0.2 foreach_1.5.1 ProtGenerics_1.26.0
[145] Biostrings_2.62.0 spatstat.core_2.3-2 GOSemSim_2.20.0
[148] rsvd_1.0.5 ScaledMatrix_1.2.0 memoise_2.0.1
[151] evaluate_0.14 tzdb_0.2.0 callr_3.7.0
[154] ps_1.6.0 curl_4.3.2 fansi_1.0.2
[157] tensor_1.5 cachem_1.0.6 deldir_1.0-6
[160] metapod_1.2.0 rjson_0.2.21 rstatix_0.7.0
[163] ggrepel_0.9.1 clue_0.3-60 rprojroot_2.0.2
[166] tools_4.1.2 magrittr_2.0.2 RCurl_1.98-1.5
[169] ape_5.6-1 broom.helpers_1.6.0 ggplotify_0.1.0
[172] xml2_1.3.3 httr_1.4.2 assertthat_0.2.1
[175] rmarkdown_2.11 globals_0.14.0 R6_2.5.1
[178] Rhdf5lib_1.16.0 progress_1.2.2 KEGGREST_1.34.0
[181] treeio_1.18.1 gtools_3.9.2 shape_1.4.6
[184] statmod_1.4.36 beachmat_2.10.0 HDF5Array_1.22.1
[187] rhdf5_2.38.0 splines_4.1.2 ggfun_0.0.4
[190] colorspace_2.0-2 generics_0.1.2 pillar_1.7.0
[193] tweenr_1.0.2 GenomeInfoDbData_1.2.7 plyr_1.8.6
[196] gtable_0.3.0 restfulr_0.0.13 knitr_1.37
[199] shadowtext_0.1.1 fastmap_1.1.0 doParallel_1.0.16
[202] broom_0.7.12 openssl_1.4.6 scales_1.1.1
[205] filelock_1.0.2 backports_1.4.1 enrichplot_1.14.1
[208] hms_1.1.1 ggforce_0.3.3 Rtsne_0.15
[211] shiny_1.7.1 polyclip_1.10-0 lazyeval_0.2.2
[214] crayon_1.4.2 MASS_7.3-55 downloader_0.4
[217] sparseMatrixStats_1.6.0 viridis_0.6.2 rpart_4.1.16
[220] compiler_4.1.2 spatstat.geom_2.3-1

[dnarna909]

Acutally, I also get the same error for computeElasticPrincipalTree(). See below:

TreeEPG <- computeElasticPrincipalTree(X = tree.data.small$data, NumNodes = 60, Lambda = .03, Mu = .01, nReps = 10, drawAccuracyComplexity = FALSE, drawEnergy = FALSE) [1] "Generating the initial configuration" [1] "Creating a chain in the 1st PC with 2 nodes" [1] "Constructing tree 1 of 10 / Subset 1 of 1" [1] "Performing PCA on the data" [1] "Using standard PCA" [1] "50 dimensions are being used" [1] "100% of the original variance has been retained" [1] "The elastic matrix is being used. Edge configuration will be ignored" [1] "Computing EPG with 60 nodes on 250 points and 50 dimensions" [1] "Using a single core" Nodes = 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD 1|0|3|17||60 775.3 60 59 10 17 0 0 726.6 726.5 0.4103 0.4104 47.97 0.7637 45.82 2749 0 11.658 sec elapsed

Error in 1:ncol(AllComb) : argument of length 0