Closed Hofphi closed 3 hours ago
Hi,
thank you very much for this great tool. I am finally able to generate informative plots in a fast manner.
However, I have an issue related to ggVennDiagram when using ClonalResidencyPlot() with 'type=upset':
_Error: 'vennregionlabel' is not an exported object from 'namespace:ggVennDiagram'
data(contig_list, package = "scRepertoire") data <- scRepertoire::combineTCR(contig_list, samples = c("P17B", "P17L", "P18B", "P18L", "P19B","P19L", "P20B", "P20L") ) data <- scRepertoire::addVariable(data, variable.name = "Type", variables = rep(c("B", "L"), 4) ) data <- scRepertoire::addVariable(data, variable.name = "Subject", variables = rep(c("P17", "P18", "P19", "P20"), each = 2) ) ClonalResidencyPlot(data, plot_type = "upset", groups = c("P18B", "P18L")) Error: 'venn_regionlabel' is not an exported object from 'namespace:ggVennDiagram'
I would very much appreciate your help.
Here is my session info:
R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 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; LAPACK version 3.10.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] scplotter_0.1.0 dplyr_1.1.4 scRepertoire_2.0.8 ggplot2_3.5.1 Seurat_5.0.1 SeuratObject_5.0.0 sp_2.1-4 loaded via a namespace (and not attached): [1] cubature_2.1.0 RcppAnnoy_0.0.22 splines_4.3.0 later_1.3.2 bitops_1.0-7 [6] tibble_3.2.1 polyclip_1.10-6 janitor_2.2.0 fastDummies_1.7.3 lifecycle_1.0.4 [11] sf_1.0-6 globals_0.16.3 lattice_0.22-5 MASS_7.3-60 magrittr_2.0.3 [16] plotly_4.10.4 httpuv_1.6.15 sctransform_0.4.1 spam_2.10-0 spatstat.sparse_3.0-3 [21] reticulate_1.37.0 DBI_1.1.3 cowplot_1.1.3 pbapply_1.7-2 RColorBrewer_1.1-3 [26] lubridate_1.9.3 abind_1.4-5 zlibbioc_1.48.0 BuenColors_0.5.6 Rtsne_0.17 [31] GenomicRanges_1.54.1 purrr_1.0.2 ggraph_2.1.0 BiocGenerics_0.48.1 RCurl_1.98-1.13 [36] hash_2.2.6.3 tweenr_2.0.2 evmix_2.12 circlize_0.4.16 GenomeInfoDbData_1.2.11 [41] IRanges_2.36.0 S4Vectors_0.40.1 ggrepel_0.9.6 irlba_2.3.5.1 listenv_0.9.1 [46] spatstat.utils_3.0-4 units_0.8-4 iNEXT_3.0.1 MatrixModels_0.5-3 goftest_1.2-3 [51] RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1 leiden_0.4.3.1 [56] codetools_0.2-19 DelayedArray_0.28.0 scCustomize_2.0.0 xml2_1.3.6 ggforce_0.4.1 [61] tidyselect_1.2.1 shape_1.4.6.1 farver_2.1.2 viridis_0.6.4 matrixStats_1.3.0 [66] stats4_4.3.0 spatstat.explore_3.2-7 jsonlite_1.8.8 e1071_1.7-14 tidygraph_1.2.3 [71] progressr_0.14.0 ggridges_0.5.6 ggalluvial_0.12.5 survival_3.5-7 ggnewscale_0.5.0 [76] tools_4.3.0 stringdist_0.9.10 ica_1.0-3 ggVennDiagram_1.2.3 Rcpp_1.0.13 [81] glue_1.8.0 gridExtra_2.3 SparseArray_1.2.2 MatrixGenerics_1.14.0 GenomeInfoDb_1.38.1 [86] withr_3.0.1 fastmap_1.2.0 fansi_1.0.6 SparseM_1.81 digest_0.6.35 [91] timechange_0.2.0 R6_2.5.1 mime_0.12 ggprism_1.0.4 colorspace_2.1-1 [96] scattermore_1.2 tensor_1.5 spatstat.data_3.0-4 utf8_1.2.4 tidyr_1.3.1 [101] generics_0.1.3 data.table_1.15.4 class_7.3-22 graphlayouts_1.0.2 httr_1.4.7 [106] htmlwidgets_1.6.4 S4Arrays_1.2.0 uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.5 [111] lmtest_0.9-40 SingleCellExperiment_1.24.0 XVector_0.42.0 htmltools_0.5.8.1 dotCall64_1.1-1 [116] scales_1.3.0 Biobase_2.62.0 png_0.1-8 snakecase_0.11.1 ggdendro_0.2.0 [121] rstudioapi_0.15.0 rjson_0.2.21 reshape2_1.4.4 nlme_3.1-163 proxy_0.4-27 [126] zoo_1.8-12 GlobalOptions_0.1.2 stringr_1.5.1 RVenn_1.1.0 KernSmooth_2.23-22 [131] parallel_4.3.0 miniUI_0.1.1.1 vipor_0.4.5 ggrastr_1.0.2 pillar_1.9.0 [136] grid_4.3.0 vctrs_0.6.5 RANN_2.6.1 VGAM_1.1-9 promises_1.3.0 [141] xtable_1.8-4 cluster_2.1.4 beeswarm_0.4.0 paletteer_1.5.0 truncdist_1.0-2 [146] cli_3.6.3 compiler_4.3.0 rlang_1.1.4 crayon_1.5.2 future.apply_1.11.2 [151] labeling_0.4.3 classInt_0.4-10 rematch2_2.1.2 plyr_1.8.9 forcats_1.0.0 [156] ggbeeswarm_0.7.2 stringi_1.8.4 viridisLite_0.4.2 deldir_2.0-4 assertthat_0.2.1 [161] munsell_0.5.1 gsl_2.1-8 lazyeval_0.2.2 spatstat.geom_3.2-9 quantreg_5.97 [166] Matrix_1.6-3 RcppHNSW_0.6.0 patchwork_1.3.0 future_1.33.2 shiny_1.8.1.1 [171] plotthis_0.3.2 SummarizedExperiment_1.32.0 evd_2.3-6.1 ROCR_1.0-11 gridtext_0.1.5 [176] igraph_2.0.3
What's going on here?
I had installed an older version of ggVennDiagram which caused the faulty behavior during ClonalResidencyPlot().
I closed the issue once I have realized that.
Sorry for the confusion.
Hi,
thank you very much for this great tool. I am finally able to generate informative plots in a fast manner.
However, I have an issue related to ggVennDiagram when using ClonalResidencyPlot() with 'type=upset':
_Error: 'vennregionlabel' is not an exported object from 'namespace:ggVennDiagram'
I would very much appreciate your help.
Here is my session info: