Genes coherently changing in the two stages in the plot (i.e. l2FC>=0.05 or <=-0.05 in both stages and with at least abs(l2FC)>=0.1 in one of the two stages) are colored and labeled.
Genes coherently changing in the two stages in the plot (i.e. l2FC>=0.05 or <=-0.05 in both stages and with at least abs(l2FC)>=0.1 in one of the two stages) are colored, genes coherently changing in all three stages (i.e. l2FC>=0.05 or <=-0.05 in all three stages and with at least abs(l2FC)>=0.1 in one of the three stages) are also labeled.
cor(DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.twocell, DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.morulae, method = "pearson")
## [1] 0.007678755
cor(DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.twocell, DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.blasto, method = "pearson")
## [1] 0.007779939
coherent_DEGs_twocell_mor_dt <- DEGs_res_all_preimpl_activeVsDead_merged[DEGs_res_all_preimpl_activeVsDead_merged$color_twocell_mor != "none"]
coherent_DEGs_twocell_blasto_dt <- DEGs_res_all_preimpl_activeVsDead_merged[DEGs_res_all_preimpl_activeVsDead_merged$color_twocell_blasto != "none"]
cor(coherent_DEGs_twocell_mor_dt$log2FoldChange.twocell, coherent_DEGs_twocell_mor_dt$log2FoldChange.morulae, method = "pearson")
## [1] 0.6118887
cor(coherent_DEGs_twocell_blasto_dt$log2FoldChange.twocell, coherent_DEGs_twocell_blasto_dt$log2FoldChange.blasto, method = "pearson")
## [1] 0.2175304
sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] gplots_3.1.3 data.table_1.14.6
## [3] ggrepel_0.9.2 ggplot2_3.4.0
## [5] DESeq2_1.34.0 SummarizedExperiment_1.24.0
## [7] Biobase_2.54.0 MatrixGenerics_1.6.0
## [9] matrixStats_0.62.0 GenomicRanges_1.46.1
## [11] GenomeInfoDb_1.30.1 IRanges_2.28.0
## [13] S4Vectors_0.32.4 BiocGenerics_0.40.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.4 sass_0.4.2 bit64_4.0.5
## [4] jsonlite_1.8.3 splines_4.1.3 gtools_3.9.3
## [7] bslib_0.4.1 assertthat_0.2.1 highr_0.9
## [10] blob_1.2.3 GenomeInfoDbData_1.2.7 yaml_2.3.6
## [13] pillar_1.8.1 RSQLite_2.2.18 lattice_0.20-45
## [16] glue_1.6.2 digest_0.6.30 RColorBrewer_1.1-3
## [19] XVector_0.34.0 colorspace_2.0-3 htmltools_0.5.3
## [22] Matrix_1.5-3 XML_3.99-0.12 pkgconfig_2.0.3
## [25] genefilter_1.76.0 zlibbioc_1.40.0 xtable_1.8-4
## [28] scales_1.2.1 BiocParallel_1.28.3 tibble_3.1.8
## [31] annotate_1.72.0 KEGGREST_1.34.0 farver_2.1.1
## [34] generics_0.1.3 withr_2.5.0 cachem_1.0.6
## [37] cli_3.4.1 survival_3.2-13 magrittr_2.0.3
## [40] crayon_1.5.2 memoise_2.0.1 evaluate_0.18
## [43] fansi_1.0.3 tools_4.1.3 lifecycle_1.0.3
## [46] stringr_1.4.1 locfit_1.5-9.6 munsell_0.5.0
## [49] DelayedArray_0.20.0 AnnotationDbi_1.56.2 Biostrings_2.62.0
## [52] compiler_4.1.3 jquerylib_0.1.4 caTools_1.18.2
## [55] rlang_1.0.6 grid_4.1.3 RCurl_1.98-1.9
## [58] rstudioapi_0.14 labeling_0.4.2 bitops_1.0-7
## [61] rmarkdown_2.18 codetools_0.2-18 gtable_0.3.1
## [64] DBI_1.1.3 R6_2.5.1 knitr_1.40
## [67] dplyr_1.0.10 fastmap_1.1.0 bit_4.0.5
## [70] utf8_1.2.2 KernSmooth_2.23-20 stringi_1.7.8
## [73] parallel_4.1.3 Rcpp_1.0.9 vctrs_0.5.1
## [76] geneplotter_1.72.0 png_0.1-7 tidyselect_1.2.0
## [79] xfun_0.35