Last updated: 2022-11-15

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Knit directory: dgrp-starve/

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Rmd ca79c22 nklimko 2022-11-15 wflow_publish("analysis/*")

# Read in tables
dtf <- fread("data/eQTL_traits_females.csv")
dtm <- fread("data/eQTL_traits_males.csv")

#Change column order to line, starvation, everything else
setcolorder(dtf, c(1,10,2:9,11:19))
#male has aggression moved to end to line up all other column indices
setcolorder(dtm, c(1,11,3:10,12:20,2))

# Bind tables on line
bound <- dtm[dtf, on=.(line)]

# create average starvation
x <- (bound[,2,with=FALSE] + bound[,21,with=FALSE]) / 2


  # AGGRESSION, male only
title <- paste("starvation resistance vs",colnames(bound[, 20, with=FALSE]))
x <- bound[,2] 
y <- bound[,20]
raw <- cbind(x,y)
clean <- setDT(raw)

varList <- rep(1:20)
for(i in 1:length(varList)) {
  varList[i] <- paste0("g",varList[i])

storage <- rep(0,20)

# Determine average of each trait
for(i in 3:19)
  title <- paste("starvation resistance vs",colnames(bound[, i, with=FALSE]))
  j <- i + 19
  y <- (bound[,i,with=FALSE] + bound[,j,with=FALSE]) / 2
  raw <- cbind(x,y)
  clean <- setDT(raw)

  colnames(clean) <- c("starvation", "trait")
  tempPlot <- ggplot(clean, aes(x=clean$starvation, y=clean$trait)) +
    geom_point() + geom_smooth(method=lm)
  #storage[i-2] <- tempPlot 
  #plot(clean, main=title)



R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/ohpc/pub/Software/openblas_0.3.10/lib/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] ggplot2_3.3.5     data.table_1.14.2 dplyr_1.0.8      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     highr_0.9        pillar_1.7.0     compiler_4.0.3  
 [5] bslib_0.3.1      later_1.3.0      jquerylib_0.1.4  git2r_0.30.1    
 [9] workflowr_1.7.0  tools_4.0.3      digest_0.6.29    gtable_0.3.0    
[13] jsonlite_1.8.0   evaluate_0.15    lifecycle_1.0.1  tibble_3.1.6    
[17] pkgconfig_2.0.3  rlang_1.0.4      DBI_1.1.2        cli_3.3.0       
[21] rstudioapi_0.13  yaml_2.3.5       xfun_0.30        fastmap_1.1.0   
[25] withr_2.5.0      stringr_1.4.0    knitr_1.38       generics_0.1.2  
[29] fs_1.5.2         vctrs_0.4.1      sass_0.4.1       grid_4.0.3      
[33] tidyselect_1.1.2 rprojroot_2.0.3  glue_1.6.2       R6_2.5.1        
[37] fansi_1.0.3      rmarkdown_2.16   purrr_0.3.4      magrittr_2.0.3  
[41] whisker_0.4      scales_1.2.0     promises_1.2.0.1 ellipsis_0.3.2  
[45] htmltools_0.5.2  assertthat_0.2.1 colorspace_2.0-3 httpuv_1.6.5    
[49] utf8_1.2.2       stringi_1.7.6    munsell_0.5.0    crayon_1.5.1