Open baj12 opened 2 months ago
Describe the bug Error in cyto_plot after renaming samples:
Error in frameList[isFrame] : invalid subscript type 'list'
To Reproduce
library(CytoExploreR) data(GvHD) set <- GvHD[1:4] cyto_channels(set) cyto_plot(set, parent = "root", channels = "FSC-H", density_stack = .5) attributes(set) ls(envir = attr(set,"frames")) pd = attr(set,"phenoData") attr(set, "subset") sampleNames(set) sampleNames(set) <- c("V1", "V2", "V3", "V4") attributes(set) ls(envir = attr(set,"frames")) cyto_plot(set, parent = "root", channels = "FSC-H", density_stack = .5) attr(set, "subset") sessionInfo() R version 4.4.1 (2024-06-14) Platform: x86_64-apple-darwin20 Running under: macOS Monterey 12.7.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Paris tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] CytoExploreR_1.1.0 openCyto_2.13.0 flowWorkspace_4.15.5 flowCore_2.15.3 loaded via a namespace (and not attached): [1] RBGL_1.78.0 remotes_2.5.0 rlang_1.1.4 magrittr_2.0.3 matrixStats_1.3.0 compiler_4.4.1 png_0.1-8 [8] callr_3.7.6 vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1 profvis_0.3.8 pkgconfig_2.0.3 fastmap_1.2.0 [15] ellipsis_0.3.2 utf8_1.2.4 promises_1.3.0 ncdfFlow_2.48.0 rmarkdown_2.27 sessioninfo_1.2.2 graph_1.80.0 [22] ps_1.7.7 purrr_1.0.2 xfun_0.46 zlibbioc_1.48.2 cachem_1.1.0 jsonlite_1.8.8 later_1.3.2 [29] parallel_4.4.1 R6_2.5.1 bslib_0.8.0 stringi_1.8.4 RColorBrewer_1.1-3 reticulate_1.38.0 pkgload_1.4.0 [36] jquerylib_0.1.4 Rcpp_1.0.13 knitr_1.48 usethis_3.0.0 zoo_1.8-12 httpuv_1.6.15 Matrix_1.7-0 [43] tidyselect_1.2.1 rstudioapi_0.16.0 yaml_2.3.10 miniUI_0.1.1.1 curl_5.2.1 processx_3.8.4 pkgbuild_1.4.4 [50] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9 Biobase_2.62.0 shiny_1.9.1 askpass_1.2.0 evaluate_0.24.0 [57] Rtsne_0.17 EmbedSOM_2.1.2 desc_1.4.3 urlchecker_1.0.1 pillar_1.9.0 flowAI_1.32.0 stats4_4.4.1 [64] generics_0.1.3 S4Vectors_0.40.2 ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0 xtable_1.8-4 glue_1.7.0 [71] changepoint_2.2.4 tools_4.4.1 robustbase_0.99-3 data.table_1.15.4 RSpectra_0.16-2 visNetwork_2.1.2 fs_1.6.4 [78] XML_3.99-0.17 grid_4.4.1 flowClust_3.40.0 tidyr_1.3.1 RProtoBufLib_2.14.1 umap_0.2.10.0 devtools_2.4.5 [85] colorspace_2.1-1 cli_3.6.3 rsvd_1.0.5 rhandsontable_0.3.8 fansi_1.0.6 cytolib_2.14.1 dplyr_1.1.4 [92] Rgraphviz_2.46.0 gtable_0.3.5 DEoptimR_1.1-3 sass_0.4.9 digest_0.6.36 BiocGenerics_0.48.1 htmlwidgets_1.6.4 [99] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4 mime_0.12 openssl_2.2.0 MASS_7.3-61 >
Expected behavior i would expect the same plot as plot 1 only with different sample names
Desktop (please complete the following information): see sessionInfo
Describe the bug Error in cyto_plot after renaming samples:
Error in frameList[isFrame] : invalid subscript type 'list'
To Reproduce
Expected behavior i would expect the same plot as plot 1 only with different sample names
Desktop (please complete the following information): see sessionInfo