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)]
colnames(bound) [1] "line" "starvation" "cafe"
[4] "chillcoma" "day.bout.number" "day.sleep"
[7] "night.bout.number" "night.sleep" "phototaxis.4day"
[10] "startle" "waking.activity" "free.glucose"
[13] "glycogen" "free.glycerol" "triglyceride"
[16] "protein" "body.weight" "thorax.length"
[19] "thorax.width" "aggression" "i.starvation"
[22] "i.cafe" "i.chillcoma" "i.day.bout.number"
[25] "i.day.sleep" "i.night.bout.number" "i.night.sleep"
[28] "i.phototaxis.4day" "i.startle" "i.waking.activity"
[31] "i.free.glucose" "i.glycogen" "i.free.glycerol"
[34] "i.triglyceride" "i.protein" "i.body.weight"
[37] "i.thorax.length" "i.thorax.width" # create average starvation
x <- (bound[,2,with=FALSE] + bound[,21,with=FALSE]) / 2
storage <- rep(0,20)
gg <- vector(mode='list', length=18)
# AGGRESSION, male only
yL <- colnames(bound[, 20, with=FALSE])
x <- bound[,2]
y <- bound[,20]
raw <- na.omit(cbind(x,y))
clean <- setDT(raw)
colnames(clean) <- c("starvation", "trait")
corCoeff <- str_sub(as.character(cor.test(clean$starvation, clean$trait)[4]), 8,16)
storage[1] <- as.numeric(corCoeff)
graphTitle <- paste0(colnames(bound[, 20, with=FALSE]),": R=",corCoeff)
gg[[1]] <- ggplot(clean, aes(x=starvation, y=trait)) +
geom_point() +
geom_smooth(formula = y ~ x, method=lm) +
labs(title = graphTitle, x="starvation",y=yL)
# 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
yL <- colnames(bound[, i, with=FALSE])
raw <- na.omit(cbind(x,y))
clean <- setDT(raw)
colnames(clean) <- c("starvation", "trait")
corCoeff <- str_sub(as.character(cor.test(clean$starvation, clean$trait)[4]), 8,16)
storage[i-1] <- as.numeric(corCoeff)
graphTitle <- paste0(colnames(bound[, i, with=FALSE]),": R=",corCoeff)
gg[[i-1]] <- ggplot(clean, aes(x=starvation, y=trait)) +
geom_point() +
geom_smooth(formula = y ~ x, method=lm) +
labs(title = graphTitle, x="starvation",y=yL)
}
par(mfrow=c(2,2))
plot_grid(gg[[1]],gg[[2]],gg[[3]],gg[[4]],ncol=2)Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-transparency is
not supported on this device: reported only once per page
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| 79e98ca | nklimko | 2022-11-15 |
plot_grid(gg[[5]],gg[[6]],gg[[7]],gg[[8]],ncol=2)Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-transparency is
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| 79e98ca | nklimko | 2022-11-15 |
plot_grid(gg[[9]],gg[[10]],gg[[11]],gg[[12]],ncol=2)Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-transparency is
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| 79e98ca | nklimko | 2022-11-15 |
plot_grid(gg[[13]],gg[[14]],gg[[15]],gg[[16]],ncol=2)Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-transparency is
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plot_grid(gg[[17]])Warning in grid.Call.graphics(C_polygon, x$x, x$y, index): semi-transparency is
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| 79e98ca | nklimko | 2022-11-15 |
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] cowplot_1.1.1 ggplot2_3.3.5 data.table_1.14.2 stringr_1.4.0
[5] dplyr_1.0.8 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] tidyselect_1.1.2 xfun_0.30 bslib_0.3.1 purrr_0.3.4
[5] lattice_0.20-45 splines_4.0.3 colorspace_2.0-3 vctrs_0.4.1
[9] generics_0.1.2 htmltools_0.5.2 mgcv_1.8-40 yaml_2.3.5
[13] utf8_1.2.2 rlang_1.0.4 later_1.3.0 pillar_1.7.0
[17] jquerylib_0.1.4 withr_2.5.0 glue_1.6.2 DBI_1.1.2
[21] lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0 evaluate_0.15
[25] labeling_0.4.2 knitr_1.38 callr_3.7.0 fastmap_1.1.0
[29] httpuv_1.6.5 ps_1.6.0 fansi_1.0.3 highr_0.9
[33] Rcpp_1.0.8.3 promises_1.2.0.1 scales_1.2.0 jsonlite_1.8.0
[37] farver_2.1.0 fs_1.5.2 digest_0.6.29 stringi_1.7.6
[41] processx_3.5.3 getPass_0.2-2 rprojroot_2.0.3 grid_4.0.3
[45] cli_3.3.0 tools_4.0.3 magrittr_2.0.3 sass_0.4.1
[49] tibble_3.1.6 crayon_1.5.1 whisker_0.4 pkgconfig_2.0.3
[53] Matrix_1.4-1 ellipsis_0.3.2 assertthat_0.2.1 rmarkdown_2.16
[57] httr_1.4.2 rstudioapi_0.13 R6_2.5.1 nlme_3.1-157
[61] git2r_0.30.1 compiler_4.0.3