Multiple Comparison of Starvation Resistance Against Other Traits
Last updated: 2022-11-15
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Knit directory: dgrp-starve/
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# 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
par(mfrow=c(2,2))
# 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)
plot(clean)
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)
plot(clean)
colnames(clean) <- c("starvation", "trait")
tempPlot <- ggplot(clean, aes(x=clean$starvation, y=clean$trait)) +
geom_point() + geom_smooth(method=lm)
#tempPlot
#storage[i-2] <- tempPlot
#plot(clean, main=title)
}
About
sessionInfo()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/libopenblas_haswellp-r0.3.10.dev.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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