This repository contains the R scripts used to create the main figures for the manuscript titled: A pan-cancer single-cell analysis of intratumoral copy number diversity and evolution.
The Rscripts folder is divided into two subfolders: Functions and Figures. Functions includes the general functions used for the CNA analysis in the paper. Figures contains detailed step-by-step R code to generate the plots for main figures 1-6. The Data folder includes the processed datasets used to plot these figures.
The raw sequencing data is available at the Sequence Read Archive (SRA) under the accession number PRJNA1013415.
Part of the R scripts were adapted from CopyKit (v0.1.0). CopyKit can be installed using the following command:
devtools::install_github(repo = "navinlabcode/copykit", ref = "f709a48")Session info:
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.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] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] VennDiagram_1.7.1 futile.logger_1.4.3 ggtree_3.2.1
[4] ComplexHeatmap_2.10.0 Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[7] org.Hs.eg.db_3.14.0 GO.db_3.14.0 OrganismDbi_1.36.0
[10] GenomicFeatures_1.46.5 AnnotationDbi_1.56.2 Biobase_2.54.0
[13] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[16] S4Vectors_0.32.3 BiocGenerics_0.40.0 maftools_2.10.05
[19] ape_5.6-2 scatterpie_0.1.8 stringr_1.5.0
[22] survival_3.3-0 survminer_0.4.9 ggpubr_0.4.0
[25] readxl_1.3.1 dplyr_1.0.8 ggplot2_3.3.6.9000
[28] reticulate_1.28
loaded via a namespace (and not attached):
[1] utf8_1.2.3 R.utils_2.11.0 tidyselect_1.2.0 RSQLite_2.2.10
[5] BiocParallel_1.28.3 munsell_0.5.0 codetools_0.2-18 withr_2.5.0
[9] colorspace_2.1-0 filelock_1.0.2 knitr_1.40 rstudioapi_0.13
[13] ggsignif_0.6.3 labeling_0.4.2 MatrixGenerics_1.6.0 GenomeInfoDbData_1.2.7
[17] KMsurv_0.1-5 polyclip_1.10-4 bit64_4.0.5 farver_2.1.1
[21] vctrs_0.5.1 treeio_1.18.1 generics_0.1.3 lambda.r_1.2.4
[25] xfun_0.37 BiocFileCache_2.2.1 R6_2.5.1 doParallel_1.0.17
[29] clue_0.3-60 pals_1.7 bitops_1.0-7 cachem_1.0.6
[33] gridGraphics_0.5-1 DelayedArray_0.20.0 assertthat_0.2.1 BiocIO_1.4.0
[37] scales_1.2.0.9000 gtable_0.3.1 rlang_1.0.6 GlobalOptions_0.1.2
[41] splines_4.1.2 rtracklayer_1.54.0 rstatix_0.7.0 lazyeval_0.2.2
[45] dichromat_2.0-0 prismatic_1.1.0 broom_0.7.12 BiocManager_1.30.18
[49] yaml_2.3.7 abind_1.4-5 backports_1.4.1 RBGL_1.70.0
[53] tools_4.1.2 ggplotify_0.1.0 ellipsis_0.3.2 RColorBrewer_1.1-3
[57] Rcpp_1.0.10.2 progress_1.2.2 zlibbioc_1.40.0 purrr_0.3.4
[61] RCurl_1.98-1.6 prettyunits_1.1.1 GetoptLong_1.0.5 cowplot_1.1.1
[65] zoo_1.8-11 SummarizedExperiment_1.24.0 haven_2.4.3 cluster_2.1.2
[69] magrittr_2.0.3 magick_2.7.3 data.table_1.14.2 futile.options_1.0.1
[73] openxlsx_4.2.5 circlize_0.4.14 amap_0.8-18 matrixStats_0.63.0
[77] evaluate_0.20 hms_1.1.1 patchwork_1.1.2 xtable_1.8-4
[81] XML_3.99-0.10 rio_0.5.29 gridExtra_2.3 shape_1.4.6
[85] compiler_4.1.2 biomaRt_2.50.3 tibble_3.1.8 maps_3.4.0
[89] crayon_1.5.2 R.oo_1.24.0 htmltools_0.5.2 mgcv_1.8-39
[93] ggfun_0.0.6 tidyr_1.2.0 aplot_0.1.2 lubridate_1.8.0
[97] DBI_1.1.2 tweenr_1.0.2 formatR_1.11 dbplyr_2.1.1
[101] MASS_7.3-55 rappdirs_0.3.3 Matrix_1.5-3 car_3.0-11
[105] cli_3.6.0 R.methodsS3_1.8.1 forcats_0.5.1 pkgconfig_2.0.3
[109] km.ci_0.5-2 GenomicAlignments_1.30.0 foreign_0.8-82 xml2_1.3.3
[113] paletteer_1.4.0 foreach_1.5.2 XVector_0.34.0 snakecase_0.11.0
[117] yulab.utils_0.0.4 digest_0.6.30 janitor_2.1.0 graph_1.72.0
[121] Biostrings_2.62.0 rmarkdown_2.20 cellranger_1.1.0 survMisc_0.5.5
[125] tidytree_0.3.8 restfulr_0.0.15 curl_4.3.2 Rsamtools_2.10.0
[129] rjson_0.2.21 lifecycle_1.0.3 nlme_3.1-155 jsonlite_1.8.4
[133] carData_3.0-5 mapproj_1.2.8 fansi_1.0.3 pillar_1.8.1
[137] lattice_0.20-45 KEGGREST_1.34.0 fastmap_1.1.0 httr_1.4.4
[141] glue_1.6.2 zip_2.2.0 png_0.1-8 iterators_1.0.14
[145] bit_4.0.4 ggforce_0.3.3 stringi_1.7.12 rematch2_2.1.2
[149] blob_1.2.2 memoise_2.0.1
For any additional information, please contact the corresponding author via email.