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tanaylab / metacell

Metacell - Single-cell mRNA Analysis
https://tanaylab.github.io/metacell
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comp mc graph using the graph RGdb_50_graphs and K 20 Error in confu/csize2 : non-conformable arrays #73

Open ramvinay opened 2 years ago

ramvinay commented 2 years ago

Hi when I am running this command mcell_mc2d_force_knn(mc2d_id=paste0(dir.init.k,"_2dproj"),mc_id=paste0(dir.init.k,"_mc_f"), graph_id=paste0(dir.init.k,"_graphs"))

Then getting following error: comp mc graph using the graph RGdb_50_graphs and K 20 Error in confu/csize2 : non-conformable arrays

Could you please help to fix this problem?

Thank you, Ram

My sessioninfo is following: `> sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6.2

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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

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

other attached packages: [1] metacell_0.3.7 plyr_1.8.7 NetBID2_2.0.3 plotly_4.10.0 rhdf5_2.38.1
[6] kableExtra_1.3.4 rmarkdown_2.14 openxlsx_4.2.5 msigdbr_7.5.1 GSVA_1.42.0
[11] biomaRt_2.50.3 reshape_0.8.9 arm_1.12-2 MASS_7.3-57 MCMCglmm_2.33
[16] ape_5.6-2 coda_0.19-4 ordinal_2019.12-10 ComplexHeatmap_2.10.0 umap_0.2.8.0
[21] plotrix_3.8-2 plot3D_1.4 RColorBrewer_1.1-3 igraph_1.3.1 aricode_1.0.0
[26] ConsensusClusterPlus_1.58.0 DESeq2_1.34.0 tximport_1.22.0 impute_1.68.0 limma_3.50.3
[31] GEOquery_2.62.2 lme4_1.1-29 Matrix_1.4-1 ggplot2_3.3.6 slingshot_2.3.0
[36] TrajectoryUtils_1.2.0 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1
[41] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[46] matrixStats_0.62.0 princurve_2.1.6 sp_1.4-7 SeuratObject_4.1.0 Seurat_4.1.1

loaded via a namespace (and not attached): [1] rsvd_1.0.5 svglite_2.1.0 ica_1.0-2 corpcor_1.6.10 foreach_1.5.2
[6] lmtest_0.9-40 crayon_1.5.1 rhdf5filters_1.6.0 spatstat.core_2.4-4 nlme_3.1-157
[11] qlcMatrix_0.9.7 rlang_1.0.2 XVector_0.34.0 ROCR_1.0-11 irlba_2.3.5
[16] nloptr_2.0.1 extrafontdb_1.0 filelock_1.0.2 extrafont_0.18 BiocParallel_1.28.3
[21] rjson_0.2.21 bit64_4.0.5 glue_1.6.2 pheatmap_1.0.12 sctransform_0.3.3
[26] parallel_4.1.2 spatstat.sparse_2.1-1 AnnotationDbi_1.56.2 tcltk_4.1.2 spatstat.geom_2.4-0
[31] VGAM_1.1-6 tidyselect_1.1.2 fitdistrplus_1.1-8 XML_3.99-0.9 tidyr_1.2.0
[36] zoo_1.8-10 xtable_1.8-4 magrittr_2.0.3 evaluate_0.15 gdtools_0.2.4
[41] cli_3.3.0 zlibbioc_1.40.0 dbscan_1.1-10 rstudioapi_0.13 miniUI_0.1.1.1
[46] rpart_4.1.16 shiny_1.7.1 BiocSingular_1.10.0 xfun_0.31 askpass_1.1
[51] clue_0.3-60 cluster_2.1.3 KEGGREST_1.34.0 tibble_3.1.7 ggrepel_0.9.1
[56] listenv_0.8.0 Biostrings_2.62.0 png_0.1-7 future_1.25.0 withr_2.5.0
[61] bitops_1.0-7 slam_0.1-50 GSEABase_1.56.0 sparsesvd_0.2 pillar_1.7.0
[66] GlobalOptions_0.1.2 cachem_1.0.6 GetoptLong_1.0.5 DelayedMatrixStats_1.16.0 vctrs_0.4.1
[71] ellipsis_0.3.2 generics_0.1.2 rgdal_1.5-32 tools_4.1.2 munsell_0.5.0
[76] DelayedArray_0.20.0 fastmap_1.1.0 HSMMSingleCell_1.14.0 compiler_4.1.2 abind_1.4-5
[81] httpuv_1.6.5 rgeos_0.5-9 GenomeInfoDbData_1.2.7 gridExtra_2.3 edgeR_3.36.0
[86] lattice_0.20-45 deldir_1.0-6 utf8_1.2.2 later_1.3.0 dplyr_1.0.9
[91] BiocFileCache_2.2.1 jsonlite_1.8.0 scales_1.2.0 graph_1.72.0 docopt_0.7.1
[96] ScaledMatrix_1.2.0 sparseMatrixStats_1.6.0 hrbrthemes_0.8.0 pbapply_1.5-0 genefilter_1.76.0
[101] lazyeval_0.2.2 promises_1.2.0.1 doParallel_1.0.17 goftest_1.2-3 spatstat.utils_2.3-1
[106] reticulate_1.25 cowplot_1.1.1 webshot_0.5.3 Rtsne_0.16 uwot_0.1.11
[111] HDF5Array_1.22.1 survival_3.3-1 numDeriv_2016.8-1.1 yaml_2.3.5 systemfonts_1.0.4
[116] DDRTree_0.1.5 htmltools_0.5.2 memoise_2.0.1 locfit_1.5-9.5 tgconfig_0.1.2
[121] viridisLite_0.4.0 digest_0.6.29 assertthat_0.2.1 mime_0.12 rappdirs_0.3.3
[126] densityClust_0.3.2 Rttf2pt1_1.3.10 RSQLite_2.2.14 future.apply_1.9.0 misc3d_0.9-1
[131] data.table_1.14.2 blob_1.2.3 pdist_1.2.1 fastICA_1.2-3 splines_4.1.2
[136] Rhdf5lib_1.16.0 RCurl_1.98-1.6 monocle_2.22.0 hms_1.1.1 colorspace_2.0-3
[141] BiocManager_1.30.17 shape_1.4.6 Rcpp_1.0.8.3 RANN_2.6.1 circlize_0.4.15
[146] fansi_1.0.3 tzdb_0.3.0 parallelly_1.31.1 tgutil_0.1.11 R6_2.5.1
[151] ggridges_0.5.3 lifecycle_1.0.1 zip_2.2.0 curl_4.3.2 minqa_1.2.4
[156] leiden_0.4.2 RcppAnnoy_0.0.19 iterators_1.0.14 stringr_1.4.0 htmlwidgets_1.5.4
[161] tgstat_2.3.17 beachmat_2.10.0 polyclip_1.10-0 purrr_0.3.4 rvest_1.0.2
[166] mgcv_1.8-40 globals_0.15.0 openssl_2.0.1 fishpond_2.0.1 patchwork_1.1.1
[171] spatstat.random_2.2-0 tensorA_0.36.2 progressr_0.10.0 doMC_1.3.8 codetools_0.2-18
[176] FNN_1.1.3 gtools_3.9.2 prettyunits_1.1.1 ucminf_1.1-4 dbplyr_2.1.1
[181] RSpectra_0.16-1 gtable_0.3.0 DBI_1.1.2 tensor_1.5 httr_1.4.3
[186] KernSmooth_2.23-20 stringi_1.7.6 progress_1.2.2 reshape2_1.4.4 cubature_2.0.4.4
[191] annotate_1.72.0 viridis_0.6.2 Rgraphviz_2.38.0 xml2_1.3.3 combinat_0.0-8
[196] colorRamps_2.3.1 boot_1.3-28 readr_2.1.2 geneplotter_1.72.0 scattermore_0.8
[201] bit_4.0.4 spatstat.data_2.2-0 babelgene_22.3 pkgconfig_2.0.3 knitr_1.39 `

Lil-Psilocybe commented 2 months ago

Hello! Did you happen to ever find the error for this? I am currently experiencing the same. Thank you!