An R/C++ implementation of the Growing Neural Gas algorithm
I try to plot GNG graph:
data(iris)
iris2 <- as.matrix(iris[,1:4])
a <- gng(iris2, max_iter = 20000, epsilon_b = 0.05, epsilon_n = 0.001, age_max = 200, max_nodes = 30, lambda = 200, alpha = 0.5, beta = 0.99, assign_cluster = T, verbose = T, make_logs = F, cpp = T)
flowsomlike_plot(a, iris[,5], max.size = 0.075)
NULL
flowsomlike_plot(gng_fit = a, labels = iris[,5], max.size = 0.075)
NULL
How to vizualize it?
Hi,
I was installing a package which is dependent to "gnn".
Faced an issue of incompatibility of "gnn" release and my version of R.
Installing package into ‘/.../renv/library/R-4.2/x86_64-pc-linux-gnu’
(as ‘lib’ is unspecified)
ERROR: dependency ‘gng’ is not available for package ‘TInGa’
* removing ‘/.../renv/library/R-4.2/x86_64-pc-linux-gnu/TInGa’
Warning messages:
1: package ‘gng’ is not available for this version of R
Is there a chance to overcome this problem or recompile the gnn for R v4.2.1 ?
Thanks in advance.
Best,
Rüçhan.
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] RColorBrewer_1.1-3 slingshot_2.5.2 TrajectoryUtils_1.4.0 princurve_2.1.6
[5] SingleCellExperiment_1.18.1 SummarizedExperiment_1.26.1 Biobase_2.56.0 GenomicRanges_1.48.0
[9] GenomeInfoDb_1.32.4 IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.42.0
[13] MatrixGenerics_1.8.1 matrixStats_0.62.0 sp_1.5-0 SeuratObject_4.1.2
[17] Seurat_4.2.0 qs_0.25.4
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.26 tidyselect_1.2.0 htmlwidgets_1.5.4 grid_4.2.1
[6] Rtsne_0.16 devtools_2.4.5 munsell_0.5.0 codetools_0.2-18 ica_1.0-3
[11] future_1.28.0 miniUI_0.1.1.1 withr_2.5.0 spatstat.random_2.2-0 colorspace_2.0-3
[16] progressr_0.11.0 knitr_1.40 rstudioapi_0.14 ROCR_1.0-11 ggsignif_0.6.3
[21] tensor_1.5 listenv_0.8.0 labeling_0.4.2 GenomeInfoDbData_1.2.8 polyclip_1.10-0
[26] farver_2.1.1 pheatmap_1.0.12 rprojroot_2.0.3 parallelly_1.32.1 vctrs_0.4.2
[31] generics_0.1.3 xfun_0.33 dittoSeq_1.9.3 R6_2.5.1 ggbeeswarm_0.6.0
[36] cachem_1.0.6 bitops_1.0-7 spatstat.utils_2.3-1 DelayedArray_0.22.0 assertthat_0.2.1
[41] promises_1.2.0.1 scales_1.2.1 rgeos_0.5-9 beeswarm_0.4.0 gtable_0.3.1
[46] globals_0.16.1 processx_3.7.0 goftest_1.2-3 rlang_1.0.6 GlobalOptions_0.1.2
[51] splines_4.2.1 rstatix_0.7.0 rgdal_1.5-32 lazyeval_0.2.2 spatstat.geom_2.4-0
[56] broom_1.0.1 yaml_2.3.5 reshape2_1.4.4 abind_1.4-5 backports_1.4.1
[61] httpuv_1.6.6 usethis_2.1.6 tools_4.2.1 ggplot2_3.3.6 ellipsis_0.3.2
[66] spatstat.core_2.4-4 sessioninfo_1.2.2 ggridges_0.5.4 Rcpp_1.0.9 plyr_1.8.7
[71] sparseMatrixStats_1.8.0 zlibbioc_1.42.0 purrr_0.3.5 RCurl_1.98-1.9 prettyunits_1.1.1
[76] ps_1.7.1 ggpubr_0.4.0.999 rpart_4.1.16 deldir_1.0-6 pbapply_1.5-0
[81] viridis_0.6.2 urlchecker_1.0.1 cowplot_1.1.1 zoo_1.8-11 ggrepel_0.9.1
[86] cluster_2.1.4 fs_1.5.2 here_1.0.1 magrittr_2.0.3 data.table_1.14.2
[91] scattermore_0.8 circlize_0.4.15 lmtest_0.9-40 RANN_2.6.1 fitdistrplus_1.1-8
[96] pkgload_1.3.0 stringfish_0.15.7 patchwork_1.1.2 mime_0.12 evaluate_0.17
[101] xtable_1.8-4 gridExtra_2.3 shape_1.4.6 compiler_4.2.1 tibble_3.1.8
[106] colorway_0.2.0 crayon_1.5.2 KernSmooth_2.23-20 htmltools_0.5.3 mgcv_1.8-40
[111] later_1.3.0 ggprism_1.0.3.9000 scCustomize_0.7.0 tidyr_1.2.1 RcppParallel_5.1.5
[116] lubridate_1.8.0 DBI_1.1.3 RApiSerialize_0.1.2 MASS_7.3-58.1 Matrix_1.5-1
[121] car_3.1-0 cli_3.4.1 parallel_4.2.1 igraph_1.3.5 forcats_0.5.2
[126] pkgconfig_2.0.3 plotly_4.10.0 spatstat.sparse_2.1-1 paletteer_1.4.1 vipor_0.4.5
[131] XVector_0.36.0 snakecase_0.11.0 callr_3.7.2 stringr_1.4.1 digest_0.6.29
[136] sctransform_0.3.5 RcppAnnoy_0.0.19 janitor_2.1.0 spatstat.data_2.2-0 rmarkdown_2.17
[141] leiden_0.4.3 uwot_0.1.14 DelayedMatrixStats_1.18.1 curl_4.3.3 shiny_1.7.2
[146] lifecycle_1.0.3 nlme_3.1-160 jsonlite_1.8.2 carData_3.0-5 viridisLite_0.4.1
[151] fansi_1.0.3 pillar_1.8.1 lattice_0.20-45 pkgbuild_1.3.1 ggrastr_1.0.1
[156] fastmap_1.1.0 httr_1.4.4 survival_3.4-0 remotes_2.4.2 glue_1.6.2
[161] png_0.1-7 profvis_0.3.7 stringi_1.7.8 rematch2_2.1.2 memoise_2.0.1
[166] renv_0.16.0 dplyr_1.0.10 irlba_2.3.5.1 future.apply_1.9.1
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