Last updated: 2022-04-26

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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

Unstaged changes:
    Deleted:    aln.fa
    Modified:   data/Lost_present_gene_lists/Genes_lost_in_A_antarctica_not_other_seagrasses.txt
    Modified:   data/Lost_present_gene_lists/Genes_lost_in_P_australis_not_other_seagrasses.txt
    Modified:   data/Lost_present_gene_lists/Genes_lost_in_Z_marina_not_other_seagrasses.txt
    Modified:   data/Lost_present_gene_lists/Genes_lost_in_Z_muelleri_not_other_seagrasses.txt
    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
    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
    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
    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
    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_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
    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

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/GO_and_ortho.Rmd) and HTML (docs/GO_and_ortho.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
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)
Warning: package 'tidyverse' was built under R version 4.1.2
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 4.1.2
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
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
Warning: ggrepel: 1 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: 1 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
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_2.1.2     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_1.6.2         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_2.5.0        cli_3.2.0          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