Main text figure 5
#pdf("test.pdf", width = 15, height = 12)
plot_grid(plot_grid(del11qVolcano, del11qBox, ncol = 2, rel_widths = c(0.45,0.55),
labels = c("A","B"), label_size = 20),
geneCoordPlot,
ncol=1, rel_heights = c(0.55,0.45), labels = c("","C"), label_size = 20)
#dev.off()
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.15.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] latex2exp_0.4.0 forcats_0.5.0
[3] stringr_1.4.0 dplyr_1.0.0
[5] purrr_0.3.4 readr_1.3.1
[7] tidyr_1.1.0 tibble_3.0.3
[9] tidyverse_1.3.0 cowplot_1.0.0
[11] ggbeeswarm_0.6.0 pheatmap_1.0.12
[13] ggraph_2.0.3 ggplot2_3.3.2
[15] igraph_1.2.5 tidygraph_1.2.0
[17] DESeq2_1.26.0 SummarizedExperiment_1.16.1
[19] DelayedArray_0.12.3 BiocParallel_1.20.1
[21] matrixStats_0.56.0 Biobase_2.46.0
[23] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[25] IRanges_2.20.2 S4Vectors_0.24.4
[27] BiocGenerics_0.32.0 limma_3.42.2
loaded via a namespace (and not attached):
[1] shinydashboard_0.7.1 tidyselect_1.1.0 RSQLite_2.2.0
[4] AnnotationDbi_1.48.0 htmlwidgets_1.5.1 grid_3.6.0
[7] maxstat_0.7-25 munsell_0.5.0 codetools_0.2-16
[10] DT_0.14 withr_2.2.0 colorspace_1.4-1
[13] knitr_1.29 rstudioapi_0.11 ggsignif_0.6.0
[16] labeling_0.3 git2r_0.27.1 slam_0.1-47
[19] GenomeInfoDbData_1.2.2 KMsurv_0.1-5 polyclip_1.10-0
[22] bit64_0.9-7 farver_2.0.3 rprojroot_1.3-2
[25] vctrs_0.3.1 generics_0.0.2 TH.data_1.0-10
[28] xfun_0.15 sets_1.0-18 R6_2.4.1
[31] graphlayouts_0.7.0 locfit_1.5-9.4 bitops_1.0-6
[34] fgsea_1.12.0 assertthat_0.2.1 promises_1.1.1
[37] scales_1.1.1 multcomp_1.4-13 nnet_7.3-14
[40] beeswarm_0.2.3 gtable_0.3.0 sandwich_2.5-1
[43] workflowr_1.6.2 rlang_0.4.7 genefilter_1.68.0
[46] splines_3.6.0 rstatix_0.6.0 acepack_1.4.1
[49] broom_0.7.0 checkmate_2.0.0 yaml_2.2.1
[52] abind_1.4-5 modelr_0.1.8 crosstalk_1.1.0.1
[55] backports_1.1.8 httpuv_1.5.4 Hmisc_4.4-0
[58] tools_3.6.0 relations_0.6-9 ellipsis_0.3.1
[61] gplots_3.0.4 RColorBrewer_1.1-2 Rcpp_1.0.5
[64] visNetwork_2.0.9 base64enc_0.1-3 zlibbioc_1.32.0
[67] RCurl_1.98-1.2 ggpubr_0.4.0 rpart_4.1-15
[70] viridis_0.5.1 zoo_1.8-8 haven_2.3.1
[73] ggrepel_0.8.2 cluster_2.1.0 exactRankTests_0.8-31
[76] fs_1.4.2 magrittr_1.5 data.table_1.12.8
[79] openxlsx_4.1.5 survminer_0.4.7 reprex_0.3.0
[82] mvtnorm_1.1-1 hms_0.5.3 shinyjs_1.1
[85] mime_0.9 evaluate_0.14 xtable_1.8-4
[88] XML_3.98-1.20 rio_0.5.16 jpeg_0.1-8.1
[91] readxl_1.3.1 gridExtra_2.3 compiler_3.6.0
[94] KernSmooth_2.23-17 crayon_1.3.4 htmltools_0.5.0
[97] mgcv_1.8-31 later_1.1.0.1 Formula_1.2-3
[100] geneplotter_1.64.0 lubridate_1.7.9 DBI_1.1.0
[103] tweenr_1.0.1 dbplyr_1.4.4 MASS_7.3-51.6
[106] jyluMisc_0.1.5 Matrix_1.2-18 car_3.0-8
[109] cli_2.0.2 marray_1.64.0 gdata_2.18.0
[112] km.ci_0.5-2 pkgconfig_2.0.3 foreign_0.8-71
[115] piano_2.2.0 xml2_1.3.2 annotate_1.64.0
[118] vipor_0.4.5 XVector_0.26.0 drc_3.0-1
[121] rvest_0.3.5 digest_0.6.25 rmarkdown_2.3
[124] cellranger_1.1.0 fastmatch_1.1-0 survMisc_0.5.5
[127] htmlTable_2.0.1 curl_4.3 shiny_1.5.0
[130] gtools_3.8.2 nlme_3.1-148 lifecycle_0.2.0
[133] jsonlite_1.7.0 carData_3.0-4 viridisLite_0.3.0
[136] fansi_0.4.1 pillar_1.4.6 lattice_0.20-41
[139] fastmap_1.0.1 httr_1.4.1 plotrix_3.7-8
[142] survival_3.2-3 glue_1.4.1 zip_2.0.4
[145] png_0.1-7 bit_1.1-15.2 ggforce_0.3.2
[148] stringi_1.4.6 blob_1.2.1 latticeExtra_0.6-29
[151] caTools_1.18.0 memoise_1.1.0