Visualising gene differences based on read alignments
Philipp Bayer
9th March 2022
Last updated: 2023-11-22
Checks: 6 1
Knit directory:
Amphibolis_Posidonia_Comparison/
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Unstaged changes:
Modified: analysis/GO_and_ortho.Rmd
Modified: analysis/GOenrichment.Rmd
Modified: analysis/index.Rmd
Modified: analysis/metagenome.Rmd
Modified: data/Lost_present_gene_lists/Genes_only_in_Algae.txt
Modified: data/Lost_present_gene_lists/Genes_only_in_Aquatics_and_Seagrasses.txt
Modified: data/Lost_present_gene_lists/Genes_only_in_Aquatics_and_Seagrasses_and_Terrestrials.txt
Modified: data/Lost_present_gene_lists/Genes_only_in_Duckweeds.txt
Modified: data/Lost_present_gene_lists/Genes_only_in_Seagrasses.txt
Modified: data/Lost_present_gene_lists/Genes_only_in_Terrestrials.txt
Modified: data/Lost_present_gene_lists/Genes_union_of_Seagrass_and_Aquatics_union.txt
Modified: data/arabidopsis_gene_level_comparison.xlsx
Modified: data/arabidopsis_gene_level_comparison_only_losts.xlsx
Modified: data/arabidopsis_gene_level_counts.xlsx
Modified: output/GO_results_genes_in_Algae_NOT_Duckweeds_NOT_Seagrasses_NOT_Terrestrials.csv.png
Modified: output/GO_results_genes_in_Aquatics_NOT_Seagrasses_NOT_Terrestrials.csv.png
Modified: output/GO_results_genes_in_Aquatics_and_Seagrasses_NOT_Terrestrials.csv.png
Modified: output/GO_results_genes_in_Duckweeds_NOT_Algae_NOT_Seagrasses_NOT_Terrestrials.csv.png
Modified: output/GO_results_genes_in_Seagrasses_NOT_Algae_NOT_Duckweeds_NOT_Terrestrials.csv.png
Modified: output/GO_results_genes_in_Seagrasses_NOT_Aquatics_NOT_Terrestrials.csv.png
Modified: output/GO_results_genes_in_Terrestrials_NOT_Aquatics_NOT_Seagrasses.csv.png
Modified: output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_intersect.csv.png
Modified: output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_union.csv.png
Modified: output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv.png
Modified: output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_union.csv.png
Modified: output/GO_results_genes_lost_A_antarctica_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_lost_P_australis_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_lost_Z_marina_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_lost_Z_muelleri_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_only_P_australis_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_only_Z_marina_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_only_Z_muelleri_not_other_seagrasses.csv.png
Modified: output/GO_results_genes_union_Aquatics_and_Seagrasses_NOT_Terrestrials.csv.png
Modified: output/GO_results_terrestrials_vs_union_aquatics_seagrasses.png
Modified: output/Lost_GO_terms_in_five_species.PlantSpecific.xlsx
Modified: output/Lost_GO_terms_in_five_species.xlsx
Modified: output/Seagrasses_shared_lost_genes.xlsx
Modified: output/all_GO_plots.Rdata
Modified: output/group_venn_image.Rdata
Modified: output/seagrass_venn_image.Rdata
Staged changes:
Modified: output/patchwork_seagrass_gene_loss.png
Modified: output/patchwork_terrestrials_gene_loss.png
New: output/patchwork_terrestrials_seagrasses_gene_loss.png
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | cf53a43 | Philipp Bayer | 2022-04-26 | Build site. |
| html | 663dcbc | Philipp Bayer | 2022-03-10 | Build site. |
| Rmd | d4cd865 | Philipp Bayer | 2022-03-10 | make the setup blocks nicer |
| html | f2b7e81 | Philipp Bayer | 2022-03-10 | add missing files |
| html | aca07fd | Philipp Bayer | 2022-03-10 | Build site. |
| Rmd | be91c66 | Philipp Bayer | 2022-03-10 | GO-term updates! more groups! for the price of one! |
| Rmd | 2edd81b | Philipp Bayer | 2022-03-09 | add more ifles |
library(tidyverse)
library(patchwork)
library(wesanderson)
library(RColorBrewer)
library(UpSetR)
library(kableExtra)
library(ggVennDiagram)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())In this one I just merge some plots from the Orthofinder and GO enrichment Rmds, which I have saved as Rdata objects.
load('output/all_GO_plots.Rdata')load('output/group_venn_image.Rdata')
load('output/seagrass_venn_image.Rdata')group_venn
seagrass_venn
OK now we can make patchworks with these Venn diagrams and their associated GO-terms
sum1 <- group_venn / (plot_list$GO_results_genes_in_Terrestrials_NOT_Aquatics_NOT_Seagrasses.csv + theme(legend.position="bottom")) + plot_annotation(tag_levels = 'A') +plot_layout(heights=c(1.5,1))
sum1Warning: ggrepel: 32 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
cowplot::save_plot(sum1, filename = 'output/patchwork_terrestrials_gene_loss.png', base_height = 10, base_width = 8)Warning: ggrepel: 33 unlabeled data points (too many overlaps). Consider
increasing max.overlapssum2 <- seagrass_venn / (plot_list$GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv + theme(legend.position="bottom")) + plot_annotation(tag_levels = 'A') +plot_layout(heights=c(1.5,1))
sum2
cowplot::save_plot(sum2, filename = 'output/patchwork_seagrass_gene_loss.png', base_height = 10, base_width = 8)a <- group_venn
b <- plot_list$GO_results_genes_in_Terrestrials_NOT_Aquatics_NOT_Seagrasses.csv
c <- seagrass_venn
d <- plot_list$GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv
sum3 <- (a + c) / (b + d) +
plot_annotation(tag_levels = 'A') +
plot_layout(heights=c(1, 1.5))
sum3Warning: ggrepel: 38 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
cowplot::save_plot(sum3, filename = 'output/patchwork_terrestrials_seagrasses_gene_loss.png', base_height = 10)Warning: ggrepel: 25 unlabeled data points (too many overlaps). Consider
increasing max.overlapssum2 <- seagrass_venn / (plot_list$GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv + theme(legend.position="bottom")) + plot_annotation(tag_levels = 'A') +plot_layout(heights=c(1.5,1))
sum2
cowplot::save_plot(sum2, filename = 'output/patchwork_seagrass_gene_loss.png', base_height = 10, base_width = 8)
sessionInfo()R version 4.3.2 (2023-10-31)
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_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
time zone: Australia/Perth
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] ggVennDiagram_1.2.3 kableExtra_1.3.4 UpSetR_1.4.0
[4] RColorBrewer_1.1-3 wesanderson_0.3.7 patchwork_1.1.2
[7] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[10] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[13] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[16] tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.14 jsonlite_1.8.4 umap_0.2.10.0
[4] magrittr_2.0.3 farver_2.1.1 rmarkdown_2.21
[7] ragg_1.2.5 fs_1.6.2 zlibbioc_1.46.0
[10] vctrs_0.6.2 memoise_2.0.1 RCurl_1.98-1.12
[13] askpass_1.1 webshot_0.5.5 htmltools_0.5.5
[16] sass_0.4.6 KernSmooth_2.23-22 bslib_0.4.2
[19] plyr_1.8.8 cachem_1.0.8 whisker_0.4.1
[22] igraph_1.5.1 mime_0.12 lifecycle_1.0.3
[25] pkgconfig_2.0.3 Matrix_1.6-2 R6_2.5.1
[28] fastmap_1.1.1 GenomeInfoDbData_1.2.10 shiny_1.8.0
[31] digest_0.6.31 colorspace_2.1-0 AnnotationDbi_1.62.2
[34] S4Vectors_0.38.1 ps_1.7.5 rprojroot_2.0.3
[37] RSpectra_0.16-1 textshaping_0.3.6 RSQLite_2.3.3
[40] labeling_0.4.2 fansi_1.0.4 timechange_0.2.0
[43] httr_1.4.6 compiler_4.3.2 proxy_0.4-27
[46] bit64_4.0.5 withr_2.5.0 DBI_1.1.3
[49] highr_0.10 openssl_2.0.6 classInt_0.4-10
[52] units_0.8-4 tools_4.3.2 httpuv_1.6.11
[55] glue_1.6.2 callr_3.7.3 GOSemSim_2.26.1
[58] promises_1.2.0.1 grid_4.3.2 sf_1.0-14
[61] getPass_0.2-2 gridBase_0.4-7 generics_0.1.3
[64] gtable_0.3.3 tzdb_0.4.0 class_7.3-22
[67] data.table_1.14.8 hms_1.1.3 xml2_1.3.4
[70] utf8_1.2.3 XVector_0.40.0 BiocGenerics_0.46.0
[73] ggrepel_0.9.4 pillar_1.9.0 later_1.3.1
[76] lattice_0.22-5 renv_1.0.2 bit_4.0.5
[79] tidyselect_1.2.0 GO.db_3.17.0 tm_0.7-11
[82] Biostrings_2.68.1 knitr_1.42 git2r_0.32.0
[85] gridExtra_2.3 NLP_0.2-1 IRanges_2.34.0
[88] svglite_2.1.2 stats4_4.3.2 xfun_0.39
[91] rrvgo_1.12.2 Biobase_2.60.0 pheatmap_1.0.12
[94] stringi_1.7.12 yaml_2.3.7 evaluate_0.21
[97] wordcloud_2.6 BiocManager_1.30.20 RVenn_1.1.0
[100] cli_3.6.1 xtable_1.8-4 reticulate_1.34.0
[103] systemfonts_1.0.4 munsell_0.5.0 processx_3.8.1
[106] jquerylib_0.1.4 treemap_2.4-4 Rcpp_1.0.10
[109] GenomeInfoDb_1.36.0 png_0.1-8 parallel_4.3.2
[112] ellipsis_0.3.2 blob_1.2.4 bitops_1.0-7
[115] viridisLite_0.4.2 slam_0.1-50 scales_1.2.1
[118] e1071_1.7-13 crayon_1.5.2 rlang_1.1.1
[121] cowplot_1.1.1 KEGGREST_1.40.1 rvest_1.0.3