Last updated: 2021-03-19

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Knit directory: soybean_exploration/

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html 3a0b3d1 Lyron Winderbaum 2021-03-18 Build site.
html bc8e79d Lyron Winderbaum 2021-03-18 Build site.
html e7acd31 Lyron Winderbaum 2021-03-18 Build site.
html b5081db Lyron Winderbaum 2021-03-11 Build site.
Rmd bf94e07 Lyron Winderbaum 2021-03-11 Initial exploration of Modern USA Lines
html bf0d5b6 Lyron Winderbaum 2021-03-11 Build site.
Rmd 3a57751 Lyron Winderbaum 2021-03-11 Initial exploration of Modern USA Lines 
# # Cleanup and Global Settings
# rm(list = ls())
# if (!is.null(sessionInfo()$otherPkgs)) {
#   invisible(lapply(paste0('package:', names(sessionInfo()$otherPkgs)), 
#                    detach, character.only=TRUE, unload=TRUE))
# }
# graphics.off()
# options(stringsAsFactors = FALSE)

library(tidyverse)
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.2.1     ✔ purrr   0.3.2
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   1.0.0     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Read in and subset data

# Read tidy data saved at the of initial_data_organisation.Rmd
load(file.path('data', 'pav_data.RData'))

# Subset to just lines with a group and country
meta.df = subset(meta.df, !is.na(Group) & !is.na(Country))
# Subset to just Modern USA lines
meta.df = subset(meta.df, Country == 'USA' & Group == "Modern cultivar")

# Reduce presence absence data
pav_table = subset(pav_table, Line %in% meta.df$Line)

# Proportion presence
hist(colMeans(pav_table[, -1]))

Version Author Date
bf0d5b6 Lyron Winderbaum 2021-03-11

NBS data

# Reduce to just NBS genes
nbs_table = pav_table[, c(TRUE, names(pav_table)[-1] %in% nbs$Name)]
# Proportion presence
hist(colMeans(nbs_table[, -1]))

Version Author Date
bf0d5b6 Lyron Winderbaum 2021-03-11

Comments

Ahh, this makes sense. It seems the Modern USA Lines are fairly homogenous in terms of genes present/ absent.


sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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       

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

other attached packages:
[1] forcats_0.4.0   stringr_1.4.0   dplyr_0.8.3     purrr_0.3.2    
[5] readr_1.3.1     tidyr_1.0.0     tibble_2.1.3    ggplot2_3.2.1  
[9] tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0 xfun_0.10        haven_2.3.1      lattice_0.20-41 
 [5] colorspace_1.4-1 vctrs_0.3.1      generics_0.0.2   htmltools_0.4.0 
 [9] yaml_2.2.0       rlang_0.4.6      later_1.0.0      pillar_1.4.2    
[13] withr_2.1.2      glue_1.3.1       modelr_0.1.5     readxl_1.3.1    
[17] lifecycle_0.1.0  munsell_0.5.0    gtable_0.3.0     workflowr_1.6.2 
[21] cellranger_1.1.0 rvest_0.3.4      evaluate_0.14    knitr_1.25      
[25] httpuv_1.5.2     broom_0.5.2      Rcpp_1.0.3       promises_1.1.0  
[29] backports_1.1.5  scales_1.0.0     jsonlite_1.6     fs_1.3.1        
[33] hms_0.5.1        digest_0.6.23    stringi_1.4.3    grid_3.6.3      
[37] rprojroot_1.3-2  cli_1.1.0        tools_3.6.3      magrittr_1.5    
[41] lazyeval_0.2.2   crayon_1.3.4     whisker_0.4      pkgconfig_2.0.3 
[45] xml2_1.2.2       lubridate_1.7.4  assertthat_0.2.1 rmarkdown_1.16  
[49] httr_1.4.1       rstudioapi_0.10  R6_2.4.0         nlme_3.1-149    
[53] git2r_0.26.1     compiler_3.6.3