Last updated: 2022-03-10

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Knit directory: Amphibolis_Posidonia_Comparison/

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/OTT.nb.html
    Ignored:    analysis/plotRgenes.nb.html

Untracked files:
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_intersect.csv
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_intersect.csv.png
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_union.csv
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_union.csv.png
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv.png
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_union.csv
    Untracked:  output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_union.csv.png

Unstaged changes:
    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_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/patchwork_seagrass_gene_loss.png
    Modified:   output/patchwork_terrestrials_gene_loss.png

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File Version Author Date Message
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)
Warning: package 'tidyverse' was built under R version 4.1.1
-- Attaching packages --------------------------------------- tidyverse 1.3.1 --
v ggplot2 3.3.5     v purrr   0.3.4
v tibble  3.1.5     v dplyr   1.0.7
v tidyr   1.1.4     v stringr 1.4.0
v readr   2.0.2     v forcats 0.5.1
Warning: package 'ggplot2' was built under R version 4.1.1
Warning: package 'tibble' was built under R version 4.1.1
Warning: package 'tidyr' was built under R version 4.1.1
Warning: package 'readr' was built under R version 4.1.1
Warning: package 'purrr' was built under R version 4.1.1
Warning: package 'dplyr' was built under R version 4.1.1
Warning: package 'stringr' was built under R version 4.1.1
Warning: package 'forcats' was built under R version 4.1.1
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
library(patchwork)
Warning: package 'patchwork' was built under R version 4.1.1
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))
sum1

cowplot::save_plot(sum1, filename = 'output/patchwork_terrestrials_gene_loss.png', base_height = 10, base_width = 8)
sum2 <- 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 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] patchwork_1.1.1 forcats_0.5.1   stringr_1.4.0   dplyr_1.0.7    
 [5] purrr_0.3.4     readr_2.0.2     tidyr_1.1.4     tibble_3.1.5   
 [9] ggplot2_3.3.5   tidyverse_1.3.1 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] httr_1.4.2         sass_0.4.0         jsonlite_1.7.2     modelr_0.1.8      
 [5] bslib_0.3.1        assertthat_0.2.1   highr_0.9          cellranger_1.1.0  
 [9] yaml_2.2.1         ggrepel_0.9.1      pillar_1.6.4       backports_1.2.1   
[13] glue_1.4.2         digest_0.6.28      promises_1.2.0.1   rvest_1.0.2       
[17] colorspace_2.0-2   cowplot_1.1.1      htmltools_0.5.2    httpuv_1.6.3      
[21] pkgconfig_2.0.3    broom_0.7.9        haven_2.4.3        scales_1.1.1      
[25] whisker_0.4        later_1.3.0        tzdb_0.1.2         git2r_0.28.0      
[29] proxy_0.4-26       generics_0.1.1     farver_2.1.0       ellipsis_0.3.2    
[33] withr_2.4.2        cli_3.0.1          magrittr_2.0.1     crayon_1.4.1      
[37] readxl_1.3.1       evaluate_0.14      fs_1.5.0           fansi_0.5.0       
[41] xml2_1.3.2         class_7.3-19       tools_4.1.0        hms_1.1.1         
[45] lifecycle_1.0.1    munsell_0.5.0      reprex_2.0.1       compiler_4.1.0    
[49] jquerylib_0.1.4    e1071_1.7-9        rlang_0.4.12       classInt_0.4-3    
[53] units_0.7-2        grid_4.1.0         rstudioapi_0.13    labeling_0.4.2    
[57] rmarkdown_2.11     gtable_0.3.0       DBI_1.1.1          R6_2.5.1          
[61] lubridate_1.8.0    knitr_1.36         fastmap_1.1.0      utf8_1.2.2        
[65] rprojroot_2.0.2    KernSmooth_2.23-20 stringi_1.7.5      Rcpp_1.0.7        
[69] vctrs_0.3.8        sf_1.0-5           dbplyr_2.1.1       tidyselect_1.1.1  
[73] xfun_0.27