Error in ggiNEXT.iNEXT of Immune receptor repertoire diversity vignette

Hello,

Platypus is a wonderful tool！ I ran into an issue with running Immune receptor repertoire diversity vignette with example data.

My command : p <- VDJ_rarefaction(VDJ, feature.columns = 'VDJ_cdr3s_aa', grouping.column = 'sample_id')

Error: Error in ggiNEXT.iNEXT(inext_object, type = rarefaction_type_dict[rarefaction.type], : invalid facet variable And my Version information is as follow:

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 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] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] dplyr_1.0.10 Platypus_3.4.1

loaded via a namespace (and not attached): [1] circlize_0.4.15 plyr_1.8.7 igraph_1.3.4 lazyeval_0.2.2 sp_1.5-0
[6] splines_4.2.0 listenv_0.8.0 scattermore_0.8 ggplot2_3.3.6 digest_0.6.29
[11] foreach_1.5.2 yulab.utils_0.0.5 htmltools_0.5.3 fansi_1.0.3 magrittr_2.0.3
[16] tensor_1.5 cluster_2.1.4 ROCR_1.0-11 remotes_2.4.2 globals_0.15.1
[21] matrixStats_0.62.0 spatstat.sparse_2.1-1 colorspace_2.0-3 ggrepel_0.9.1 crayon_1.5.2
[26] jsonlite_1.8.2 progressr_0.11.0 spatstat.data_2.2-0 survival_3.3-1 zoo_1.8-10
[31] iterators_1.0.14 ape_5.6-2 glue_1.6.2 polyclip_1.10-0 gtable_0.3.1
[36] leiden_0.4.3 future.apply_1.9.0 shape_1.4.6 abind_1.4-5 scales_1.2.1
[41] pheatmap_1.0.12 DBI_1.1.3 spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.9
[46] viridisLite_0.4.1 xtable_1.8-4 gridGraphics_0.5-1 tidytree_0.4.0 reticulate_1.26
[51] spatstat.core_2.4-4 htmlwidgets_1.5.4 httr_1.4.4 RColorBrewer_1.1-3 ellipsis_0.3.2
[56] Seurat_4.1.1 ica_1.0-3 pkgconfig_2.0.3 farver_2.1.1 ggseqlogo_0.1
[61] uwot_0.1.13 deldir_1.0-6 utf8_1.2.2 ggplotify_0.1.0 tidyselect_1.2.0
[66] labeling_0.4.2 rlang_1.0.4 reshape2_1.4.4 later_1.3.0 munsell_0.5.0
[71] tools_4.2.0 cli_3.4.1 generics_0.1.3 ggridges_0.5.4 stringr_1.4.0
[76] fastmap_1.1.0 goftest_1.2-3 ggtree_3.4.2 fs_1.5.2 fitdistrplus_1.1-8
[81] purrr_0.3.5 RANN_2.6.1 pbapply_1.5-0 future_1.27.0 nlme_3.1-158
[86] mime_0.12 aplot_0.1.6 compiler_4.2.0 rstudioapi_0.14 plotly_4.10.0
[91] png_0.1-7 spatstat.utils_2.3-1 treeio_1.20.2 tibble_3.1.8 stringi_1.7.8
[96] rgeos_0.5-9 lattice_0.20-45 Matrix_1.5-1 vegan_2.6-2 permute_0.9-7
[101] vctrs_0.4.2 stringdist_0.9.8 pillar_1.8.1 lifecycle_1.0.1 BiocManager_1.30.18
[106] spatstat.geom_2.4-0 lmtest_0.9-40 GlobalOptions_0.1.2 RcppAnnoy_0.0.19 data.table_1.14.4
[111] cowplot_1.1.1 irlba_2.3.5.1 httpuv_1.6.6 patchwork_1.1.2 R6_2.5.1
[116] promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3 parallelly_1.32.1 codetools_0.2-18
[121] MASS_7.3-58.1 assertthat_0.2.1 withr_2.5.0 SeuratObject_4.1.2 iNEXT_3.0.0
[126] sctransform_0.3.4 mgcv_1.8-40 parallel_4.2.0 grid_4.2.0 rpart_4.1.16
[131] ggfun_0.0.6 tidyr_1.2.1 Rtsne_0.16 shiny_1.7.2

I'm really at a loss as to how to proceed, and any guidance would be much appreciated! Thank you for your kind help!

alexyermanos / Platypus

Error in ggiNEXT.iNEXT of Immune receptor repertoire diversity vignette #31