Last updated: 2020-09-18

Checks: 6 1

Knit directory: R_gene_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20200917) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 7b1cd32. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/eda.Rmd
    Untracked:  analysis/first-analysis.Rmd
    Untracked:  data/Lee.NBS.candidates.lst
    Untracked:  data/Lee.RGA.candidates.lst
    Untracked:  data/Lee.RLK.candidates.lst
    Untracked:  data/Lee.RLP.candidates.lst
    Untracked:  data/Lee.TMCC.candidates.lst
    Untracked:  data/Lee.pan.v1.renamed.gff
    Untracked:  data/Lee.preRGA.candidates.by.Blast.lst
    Untracked:  data/Table_of_cultivar_groups.csv
    Untracked:  data/soybean_pan_pav.matrix_gene.txt

Unstaged changes:
    Modified:   analysis/index.Rmd

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.


There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.


library(tidyverse)
-- Attaching packages ------------------------------------------------------------------------------------------------------------------ tidyverse 1.3.0 --
v ggplot2 3.3.2     v purrr   0.3.4
v tibble  3.0.2     v dplyr   1.0.0
v tidyr   1.1.0     v stringr 1.4.0
v readr   1.3.1     v forcats 0.5.0
-- Conflicts --------------------------------------------------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
library(knitr)

Introduction

Here i make some of the tables for the manuscript.

files_to_make_tables_for <- list.files(path = './data', pattern = '*lst')
files_to_make_tables_for
[1] "Lee.NBS.candidates.lst"             "Lee.preRGA.candidates.by.Blast.lst"
[3] "Lee.RGA.candidates.lst"             "Lee.RLK.candidates.lst"            
[5] "Lee.RLP.candidates.lst"             "Lee.TMCC.candidates.lst"           

The following will print warnings because I assume 3 columns, but some files have only 2:

[1] “Lee.NBS.candidates.lst”
Var1 Freq
CN 13
CNL 123
NBS 52
NL 95
OTHER 20
TN 22
TNL 99
TX 62
[1] “Lee.preRGA.candidates.by.Blast.lst”
Var1 Freq
NA 14358
[1] “Lee.RGA.candidates.lst”
Var1 Freq
CN 13
CNL 123
NBS 52
NL 95
OTHER 20
RLK 1173
RLP 180
TM-CC 280
TN 22
TNL 99
TX 62
[1] “Lee.RLK.candidates.lst”
Var1 Freq
RLK_lrr 470
RLK_lysm 19
RLK_other_receptor 684
[1] “Lee.RLP.candidates.lst”
Var1 Freq
RLP_lrr 177
RLP_lysm 3
[1] “Lee.TMCC.candidates.lst”
Var1 Freq
TM-CC 280

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

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] knitr_1.29      forcats_0.5.0   stringr_1.4.0   dplyr_1.0.0    
 [5] purrr_0.3.4     readr_1.3.1     tidyr_1.1.0     tibble_3.0.2   
 [9] ggplot2_3.3.2   tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0 xfun_0.15        haven_2.3.1      lattice_0.20-41 
 [5] colorspace_1.4-1 vctrs_0.3.1      generics_0.0.2   htmltools_0.5.0 
 [9] yaml_2.2.1       blob_1.2.1       rlang_0.4.6      later_1.1.0.1   
[13] pillar_1.4.4     withr_2.2.0      glue_1.4.1       DBI_1.1.0       
[17] dbplyr_1.4.4     modelr_0.1.8     readxl_1.3.1     lifecycle_0.2.0 
[21] munsell_0.5.0    gtable_0.3.0     workflowr_1.6.2  cellranger_1.1.0
[25] rvest_0.3.5      evaluate_0.14    httpuv_1.5.4     fansi_0.4.1     
[29] highr_0.8        broom_0.5.6      Rcpp_1.0.5       promises_1.1.1  
[33] backports_1.1.8  scales_1.1.1     jsonlite_1.7.0   fs_1.5.0.9000   
[37] hms_0.5.3        digest_0.6.25    stringi_1.4.6    grid_3.6.3      
[41] rprojroot_1.3-2  cli_2.0.2        tools_3.6.3      magrittr_1.5    
[45] crayon_1.3.4     pkgconfig_2.0.3  ellipsis_0.3.1   xml2_1.3.2      
[49] reprex_0.3.0     lubridate_1.7.9  assertthat_0.2.1 rmarkdown_2.3   
[53] httr_1.4.1       rstudioapi_0.11  R6_2.4.1         nlme_3.1-148    
[57] git2r_0.26.1     compiler_3.6.3