get_network_graph() issue

[zhenzuo2]

When umap_method=='weighted', I got an error

Error in uwot(X = X, n_neighbors = n_neighbors, n_components = n_components, : Unknown input data format

Could you please check the format of coex_mat so that it can be used by get_umap().

"corr" or "coef" works perfect! Thanks.

[yojetsharma]

Hi, this is not related to your question, but out of curiosity were you able to were you able to run the infer_grn? if so, what version of R are you using?

[zhenzuo2]

Yes. I can run.

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats graphics grDevices utils datasets methods base

other attached packages: [1] Pando_0.5.1 tidyr_1.2.1

loaded via a namespace (and not attached): [1] fastmatch_1.1-3 plyr_1.8.7 igraph_1.3.5
[4] lazyeval_0.2.2 sp_1.5-0 splines_4.2.0
[7] BiocParallel_1.30.3 listenv_0.8.0 scattermore_0.8
[10] GenomeInfoDb_1.32.4 ggplot2_3.3.6 digest_0.6.29
[13] htmltools_0.5.3 viridis_0.6.2 fansi_1.0.3
[16] magrittr_2.0.3 tensor_1.5 cluster_2.1.4
[19] ROCR_1.0-11 Biostrings_2.64.1 globals_0.16.1
[22] graphlayouts_0.8.1 matrixStats_0.62.0 spatstat.sparse_2.1-1
[25] colorspace_2.0-3 ggrepel_0.9.1 xfun_0.33
[28] dplyr_1.0.10 crayon_1.5.1 RCurl_1.98-1.8
[31] jsonlite_1.8.0 progressr_0.11.0 spatstat.data_2.2-0
[34] survival_3.4-0 zoo_1.8-11 glue_1.6.2
[37] polyclip_1.10-0 pals_1.7 gtable_0.3.1
[40] zlibbioc_1.42.0 XVector_0.36.0 leiden_0.4.3
[43] future.apply_1.9.1 BiocGenerics_0.42.0 maps_3.4.0
[46] abind_1.4-5 scales_1.2.1 DBI_1.1.3
[49] Signac_1.8.0 spatstat.random_2.2-0 miniUI_0.1.1.1
[52] Rcpp_1.0.9 viridisLite_0.4.1 xtable_1.8-4
[55] reticulate_1.26 spatstat.core_2.4-4 mapproj_1.2.8
[58] stats4_4.2.0 htmlwidgets_1.5.4 httr_1.4.4
[61] RColorBrewer_1.1-3 ellipsis_0.3.2 Seurat_4.2.0
[64] ica_1.0-3 pkgconfig_2.0.3 farver_2.1.1
[67] uwot_0.1.14 deldir_1.0-6 utf8_1.2.2
[70] tidyselect_1.1.2 rlang_1.0.6 reshape2_1.4.4
[73] later_1.3.0 munsell_0.5.0 tools_4.2.0
[76] cli_3.4.1 generics_0.1.3 ggridges_0.5.4
[79] evaluate_0.16 stringr_1.4.1 fastmap_1.1.0
[82] yaml_2.3.5 goftest_1.2-3 knitr_1.40
[85] fitdistrplus_1.1-8 tidygraph_1.2.2 purrr_0.3.4
[88] RANN_2.6.1 ggraph_2.0.6 pbapply_1.5-0
[91] future_1.28.0 nlme_3.1-159 sparseMatrixStats_1.8.0 [94] mime_0.12 RcppRoll_0.3.0 compiler_4.2.0
[97] rstudioapi_0.14 plotly_4.10.0 png_0.1-7
[100] spatstat.utils_2.3-1 tibble_3.1.8 tweenr_2.0.2
[103] stringi_1.7.8 rgeos_0.5-9 lattice_0.20-45
[106] Matrix_1.5-1 vctrs_0.4.1 pillar_1.8.1
[109] lifecycle_1.0.2 spatstat.geom_2.4-0 lmtest_0.9-40
[112] RcppAnnoy_0.0.19 data.table_1.14.2 cowplot_1.1.1
[115] bitops_1.0-7 irlba_2.3.5 httpuv_1.6.6
[118] patchwork_1.1.2 GenomicRanges_1.48.0 R6_2.5.1
[121] promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3
[124] IRanges_2.30.1 parallelly_1.32.1 codetools_0.2-18
[127] dichromat_2.0-0.1 MASS_7.3-58.1 assertthat_0.2.1
[130] withr_2.5.0 SeuratObject_4.1.2 Rsamtools_2.12.0
[133] sctransform_0.3.5 S4Vectors_0.34.0 GenomeInfoDbData_1.2.8 [136] mgcv_1.8-40 parallel_4.2.0 grid_4.2.0
[139] rpart_4.1.16 ggpointdensity_0.1.0 rmarkdown_2.16
[142] MatrixGenerics_1.8.1 Rtsne_0.16 ggforce_0.3.4
[145] shiny_1.7.2

[joschif]

The newest version should fix this. Please let me know if it works now.

[joschif]

I'm closing this since I believe it should be resolved, but feel free to reopen if the problem persists