Closed tonypanx closed 1 month ago
ncborcherding
commented
1 month ago Thanks for reaching out.
Please make a reproducible example for this issue so I know what you are experiencing.
Also with the example, please make sure to include the output of sessionInfo()
Thanks, Nick
bshim181
commented
1 month ago Experiencing the same issue.
clonalOverlap(combined_TCR, cloneCall = "aa", method = "raw", group.by = "cluster", palette = "Reds") + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
I am grouping.by a variable called cluster, but it spits it out in sample labels. Thank you for the assistance!
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.10 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so; LAPACK version 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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] scRepertoire_2.0.6 cellXY_0.99.0 scDblFinder_1.18.0
[4] harmony_1.2.1 alevinQC_1.20.0 vctrs_0.6.5
[7] patchwork_1.2.0 scater_1.30.1 scuttle_1.12.0
[10] speckle_1.4.0 Matrix_1.6-5 fishpond_2.10.0
[13] readxl_1.4.3 SingleCellExperiment_1.24.0 flexmix_2.3-19
[16] lattice_0.22-6 SeuratWrappers_0.3.19 miQC_1.12.0
[19] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4
[22] sctransform_0.4.1 glmGamPoi_1.16.0 presto_1.0.0
[25] Rcpp_1.0.12 data.table_1.15.4 viridis_0.6.5
[28] viridisLite_0.4.2 lubridate_1.9.3 forcats_1.0.0
[31] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[34] tibble_3.2.1 tidyverse_2.0.0 stringr_1.5.1
[37] dplyr_1.1.4 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 riboWaltz_2.0
[40] devtools_2.4.5 usethis_2.2.3 RSQLite_2.3.7
[43] GenomicFeatures_1.54.4 AnnotationDbi_1.64.1 hrbrthemes_0.8.7
[46] ggplot2_3.5.1 GenomicAlignments_1.38.2 Rsamtools_2.18.0
[49] SummarizedExperiment_1.32.0 Biobase_2.62.0 MatrixGenerics_1.14.0
[52] matrixStats_1.3.0 GenomicRanges_1.54.1 GenomicState_0.99.15
[55] AnnotationHub_3.10.1 BiocFileCache_2.10.2 dbplyr_2.5.0
[58] RiboProfiling_1.32.0 Biostrings_2.70.3 GenomeInfoDb_1.38.8
[61] XVector_0.42.0 IRanges_2.36.0 S4Vectors_0.40.2
[64] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] hash_2.2.6.3 igraph_2.0.3 graph_1.82.0 ica_1.0-3
[5] plotly_4.10.4 Formula_1.2-5 zlibbioc_1.48.2 tidyselect_1.2.1
[9] bit_4.0.5 rjson_0.2.21 evmix_2.12 blob_1.2.4
[13] urlchecker_1.0.1 S4Arrays_1.2.1 parallel_4.3.2 dichromat_2.0-0.1
[17] png_0.1-8 cli_3.6.2 ProtGenerics_1.34.0 goftest_1.2-3
[21] BiocIO_1.12.0 bluster_1.12.0 org.Mm.eg.db_3.18.0 BiocNeighbors_1.20.2
[25] stringdist_0.9.12 tximport_1.32.0 uwot_0.2.2 curl_5.2.1
[29] mime_0.12 evaluate_0.24.0 leiden_0.4.3.1 gsubfn_0.7
[33] stringi_1.8.4 desc_1.4.3 backports_1.5.0 gsl_2.1-8
[37] XML_3.99-0.16.1 httpuv_1.6.15 magrittr_2.0.3 rappdirs_0.3.3
[41] splines_4.3.2 ggraph_2.2.1 org.Hs.eg.db_3.19.1 DT_0.33
[45] ggbeeswarm_0.7.2 sessioninfo_1.2.2 DBI_1.2.3 withr_3.0.0
[49] svMisc_1.2.3 systemfonts_1.1.0 xgboost_1.7.7.1 lmtest_0.9-40
[53] RBGL_1.78.0 tidygraph_1.3.1 rtracklayer_1.62.0 BiocManager_1.30.23
[57] htmlwidgets_1.6.4 fs_1.6.4 biomaRt_2.58.2 ggrepel_0.9.5
[61] labeling_0.4.3 SparseArray_1.2.4 cellranger_1.1.0 extrafont_0.19
[65] reticulate_1.37.0 VariantAnnotation_1.48.1 zoo_1.8-12 GGally_2.2.1
[69] knitr_1.47 timechange_0.3.0 fansi_1.0.6 grid_4.3.2
[73] quantreg_5.98 R.oo_1.26.0 RSpectra_0.16-1 irlba_2.3.5.1
[77] extrafontdb_1.0 fastDummies_1.7.3 ellipsis_0.3.2 lazyeval_0.2.2
[81] yaml_2.3.8 survival_3.7-0 scattermore_1.2 BiocVersion_3.18.1
[85] crayon_1.5.2 RcppAnnoy_0.0.22 tweenr_2.0.3 RColorBrewer_1.1-3
[89] progressr_0.14.0 later_1.3.2 gfonts_0.2.0 ggridges_0.5.6
[93] codetools_0.2-20 base64enc_0.1-3 GlobalOptions_0.1.2 profvis_0.3.8
[97] KEGGREST_1.42.0 Rtsne_0.17 shape_1.4.6.1 limma_3.58.1
[101] gdtools_0.3.7 filelock_1.0.3 foreign_0.8-86 sqldf_0.4-11
[105] pkgconfig_2.0.3 xml2_1.3.6 evd_2.3-7 iNEXT_3.0.1
[109] spatstat.sparse_3.0-3 BSgenome_1.70.2 biovizBase_1.50.0 xtable_1.8-4
[113] plyr_1.8.9 httr_1.4.7 tools_4.3.2 globals_0.16.3
[117] pkgbuild_1.4.4 beeswarm_0.4.0 htmlTable_2.4.2 checkmate_2.3.1
[121] nlme_3.1-165 MatrixModels_0.5-3 assertthat_0.2.1 digest_0.6.35
[125] farver_2.1.2 tzdb_0.4.0 AnnotationFilter_1.26.0 reshape2_1.4.4
[129] rpart_4.1.23 crul_1.4.2 glue_1.7.0 cachem_1.1.0
[133] polyclip_1.10-6 Hmisc_5.1-3 generics_0.1.3 ggalluvial_0.12.5
[137] proto_1.0.0 parallelly_1.37.1 pkgload_1.3.4 statmod_1.5.0
[141] RcppHNSW_0.6.0 ScaledMatrix_1.10.0 fontBitstreamVera_0.1.1 pbapply_1.7-2
[145] spam_2.10-0 ggbio_1.50.0 dqrng_0.4.1 utf8_1.2.4
[149] graphlayouts_1.1.1 gtools_3.9.5 httpcode_0.3.0 gridExtra_2.3
[153] shiny_1.8.1.1 GenomeInfoDbData_1.2.11 R.utils_2.12.3 RCurl_1.98-1.14
[157] memoise_2.0.1 rmarkdown_2.27 scales_1.3.0 R.methodsS3_1.8.2
[161] future_1.33.2 RANN_2.6.1 fontLiberation_0.1.0 OrganismDbi_1.44.0
[165] spatstat.data_3.0-4 rstudioapi_0.16.0 cluster_2.1.6 spatstat.utils_3.0-4
[169] hms_1.1.3 fitdistrplus_1.1-11 munsell_0.5.1 cowplot_1.1.3
[173] colorspace_2.1-0 ggdendro_0.2.0 rlang_1.1.4 DelayedMatrixStats_1.24.0
[177] sparseMatrixStats_1.14.0 truncdist_1.0-2 dotCall64_1.1-1 shinydashboard_0.7.2
[181] ggforce_0.4.2 circlize_0.4.16 xfun_0.44 remotes_2.5.0
[185] modeltools_0.2-23 abind_1.4-5 interactiveDisplayBase_1.40.0 ps_1.7.6
[189] bitops_1.0-7 promises_1.3.0 DelayedArray_0.28.0 compiler_4.3.2
[193] prettyunits_1.2.0 beachmat_2.18.1 SparseM_1.83 listenv_0.9.1
[197] Rttf2pt1_1.3.12 fontquiver_0.2.1 edgeR_4.0.16 BiocSingular_1.18.0
[201] tensor_1.5 MASS_7.3-60.0.1 progress_1.2.3 BiocParallel_1.36.0
[205] cubature_2.1.1 spatstat.random_3.2-3 R6_2.5.1 fastmap_1.2.0
[209] vipor_0.4.7 ensembldb_2.26.0 ROCR_1.0-11 ggstats_0.6.0
[213] rsvd_1.0.5 nnet_7.3-19 gtable_0.3.5 KernSmooth_2.23-24
[217] miniUI_0.1.1.1 deldir_2.0-4 htmltools_0.5.8.1 bit64_4.0.5
[221] spatstat.explore_3.2-7 lifecycle_1.0.4 processx_3.8.4 callr_3.7.6
[225] restfulr_0.0.15 rsconnect_1.3.1 VGAM_1.1-11 spatstat.geom_3.2-9
[229] scran_1.30.2 future.apply_1.11.2 pillar_1.9.0 metapod_1.10.1
[233] locfit_1.5-9.9 jsonlite_1.8.8 chron_2.3-61 @bshim181
Is combined_TCR the output of combineTCR()? You might not have a cluster variable to "group.by"?
If not please provide the column names of your single cell object meta data.
Thanks, Nick
bshim181
commented
1 month ago Thank you so much. I was inputting outputs of combineTCR into the function. It is resolved now on my part.
tonypanx
commented
1 month ago I am working with all_combined, the result of combineTCR. I use addVariable to add a type variable to all_combined:
When I use group.by in clonalQuant to plot across type it works fine, but doesn't seem to have an effect for clonalOverlap or clonalCompare.
I think the cause of the issue may be missing handlers when group.by != NULL from clonalOverlap and clonalCompare that is present in clonalQuant such as :
if (!is.null(group.by) & !sco) { input.data <- .groupList(input.data, group.by) }
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el8-x86_64/lib/libopenblas_skylakexp-r0.3.13.so
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 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] scRepertoire_2.0.5 scales_1.3.0 ggrepel_0.9.3 scater_1.26.1 scuttle_1.8.4
[6] SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 Biobase_2.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[11] IRanges_2.32.0 S4Vectors_0.36.2 BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_1.1.0
[16] rlist_0.4.6.2 reshape2_1.4.4 ggraph_2.1.0 tidygraph_1.2.3 igraph_1.6.0
[21] RColorBrewer_1.1-3 ggthemes_4.2.4 ComplexHeatmap_2.14.0 cowplot_1.1.1 ggplotify_0.1.0
[26] SCpubr_2.0.1 rstatix_0.7.2 sctransform_0.4.1 patchwork_1.2.0 clusterProfiler_4.6.2
[31] harmony_1.2.0 Rcpp_1.0.12 stringr_1.5.1 R.utils_2.11.0 R.oo_1.24.0
[36] R.methodsS3_1.8.1 ggpubr_0.6.0 dplyr_1.1.4 plyr_1.8.9 ggplot2_3.5.1
[41] Seurat_5.0.0 SeuratObject_5.0.1 sp_1.6-0
loaded via a namespace (and not attached):
[1] rsvd_1.0.5 stringdist_0.9.10 ica_1.0-2 foreach_1.5.2 lmtest_0.9-40
[6] crayon_1.5.1 MASS_7.3-58.3 rhdf5filters_1.10.1 nlme_3.1-157 backports_1.4.1
[11] GOSemSim_2.24.0 rlang_1.1.2 XVector_0.38.0 HDO.db_0.99.1 ROCR_1.0-11
[16] irlba_2.3.5.1 SparseM_1.81 filelock_1.0.2 BiocParallel_1.32.6 rjson_0.2.21
[21] bit64_4.0.5 evmix_2.12 glue_1.6.2 parallel_4.2.0 vipor_0.4.5
[26] spatstat.sparse_3.0-0 AnnotationDbi_1.60.2 dotCall64_1.0-1 DOSE_3.24.2 spatstat.geom_3.0-6
[31] VGAM_1.1-9 tidyselect_1.2.0 fitdistrplus_1.1-8 tidyr_1.3.0 zoo_1.8-11
[36] bioc2020trajectories_0.0.0.93 xtable_1.8-4 RcppHNSW_0.4.1 MatrixModels_0.5-0 magrittr_2.0.3
[41] cli_3.6.2 zlibbioc_1.44.0 rstudioapi_0.14 miniUI_0.1.1.1 fastmatch_1.1-3
[46] treeio_1.22.0 fastDummies_1.7.3 tinytex_0.38 shiny_1.7.1 BiocSingular_1.14.0
[51] xfun_0.38 clue_0.3-65 gson_0.1.0 cluster_2.1.3 KEGGREST_1.38.0
[56] tibble_3.2.1 quantreg_5.93 ape_5.7-1 listenv_0.8.0 Biostrings_2.66.0
[61] png_0.1-7 future_1.25.0 withr_2.5.0 bitops_1.0-7 ggforce_0.4.1
[66] pillar_1.9.0 GlobalOptions_0.1.2 cachem_1.0.6 GetoptLong_1.0.5 hash_2.2.6.2
[71] DelayedMatrixStats_1.20.0 vctrs_0.6.5 ellipsis_0.3.2 generics_0.1.3 tools_4.2.0
[76] beeswarm_0.4.0 munsell_0.5.0 tweenr_1.0.2 fgsea_1.24.0 DelayedArray_0.24.0
[81] fastmap_1.1.0 compiler_4.2.0 abind_1.4-5 httpuv_1.6.5 plotly_4.10.0
[86] truncdist_1.0-2 GenomeInfoDbData_1.2.9 gridExtra_2.3 lattice_0.20-45 deldir_1.0-6
[91] utf8_1.2.2 later_1.3.0 BiocFileCache_2.6.1 jsonlite_1.8.8 princurve_2.1.6
[96] ScaledMatrix_1.6.0 tidytree_0.4.2 pbapply_1.7-2 carData_3.0-5 sparseMatrixStats_1.10.0
[101] lazyeval_0.2.2 promises_1.2.0.1 car_3.1-2 doParallel_1.0.17 goftest_1.2-3
[106] spatstat.utils_3.0-1 reticulate_1.24 Rtsne_0.16 downloader_0.4 uwot_0.1.14
[111] HDF5Array_1.26.0 survival_3.3-1 htmltools_0.5.7 memoise_2.0.1 graphlayouts_1.0.1
[116] viridisLite_0.4.0 assertthat_0.2.1 digest_0.6.29 mime_0.12 rappdirs_0.3.3
[121] spam_2.8-0 RSQLite_2.3.1 yulab.utils_0.0.6 future.apply_1.9.0 data.table_1.14.10
[126] blob_1.2.3 splines_4.2.0 labeling_0.4.2 Rhdf5lib_1.20.0 RCurl_1.98-1.12
[131] broom_1.0.4 rhdf5_2.42.1 colorspace_2.0-3 ggbeeswarm_0.7.1 shape_1.4.6
[136] aplot_0.1.10 ggrastr_1.0.2 RANN_2.6.1 circlize_0.4.15 enrichplot_1.18.4
[141] fansi_1.0.3 parallelly_1.31.1 R6_2.5.1 ggridges_0.5.3 lifecycle_1.0.4
[146] curl_4.3.2 ggsignif_0.6.3 leiden_0.3.10 Matrix_1.6-4 qvalue_2.32.0
[151] RcppAnnoy_0.0.19 iterators_1.0.14 spatstat.explore_3.0-6 htmlwidgets_1.6.2 beachmat_2.14.2
[156] polyclip_1.10-0 purrr_1.0.1 iNEXT_3.0.0 shadowtext_0.1.2 gridGraphics_0.5-1
[161] mgcv_1.8-40 globals_0.14.0 spatstat.random_3.1-3 slingshot_2.7.0 progressr_0.10.0
[166] codetools_0.2-18 GO.db_3.16.0 dbplyr_2.3.2 RSpectra_0.16-1 gtable_0.3.0
[171] DBI_1.2.3 ggalluvial_0.12.5 ggfun_0.1.4 tensor_1.5 httr_1.4.5
[176] KernSmooth_2.23-20 stringi_1.8.3 farver_2.1.0 cubature_2.1.0 viridis_0.6.2
[181] ggtree_3.9.0.001 ggdendro_0.1.23 BiocNeighbors_1.16.0 scattermore_1.2 bit_4.0.5
[186] scatterpie_0.2.1 spatstat.data_3.0-0 pkgconfig_2.0.3 TrajectoryUtils_1.6.0 gsl_2.1-8
[191] evd_2.3-6 Got the fix implemented thanks @tonypanx. For now it is in the dev branch, but will have it in the main by Friday.
Nick
tonypanx
commented
1 month ago Works now, thanks for the prompt reply and fix!
I'm encountering issues with the group.by parameter for clonalOverlap and clonalCompare. When I supply a group.by variable, the plots still default to grouping by sample. This happens both in v2.0.5 and v2.0.6