library
plot 69k scan result for m2 Novelty_residuals_RankNormal_datarelease_12182019

Last updated: 2020-02-25

Checks: 7 0

Knit directory: csna_workflow/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20190918)

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Session information: recorded

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Cache: none

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File paths: relative

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Repository version: 2fa487b

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Unstaged changes:
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    Modified:   analysis/run_09_qtlmapping.R
    Modified:   analysis/run_10_qtl_permu.R
    Modified:   analysis/run_11_qtl_blup.R

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.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	2fa487b	xhyuo	2020-02-25	four_plots_Rmd
html	0404d44	xhyuo	2020-02-25	Build site.
Rmd	259f3a5	xhyuo	2020-02-25	12_plot_69k_qtl_mapping_2.Rmd

This script will plot the qtl mapping results.

library

library(qtl2)
library(ggplot2)
load("data/Jackson_Lab_11_batches/gm_DO2816_qc.RData")
load("data/69k_grid_pgmap.RData")
pheno <- read.csv("data/pheno/Novelty_residuals_RankNormal_datarelease_12182019.csv", header = TRUE)

plot 69k scan result for m2 Novelty_residuals_RankNormal_datarelease_12182019

print("m2")

[1] "m2"

load("output/m2.69k.Novelty_residuals_RankNormal_datarelease_12182019.RData")

#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
operm <- list()
for(i in c(1:50)[c(-4,-8,-14,-15,-18,-28,-31)]){
  operm[[i]] <- get(load(paste0("output/permu/m2_69k_Novelty_residuals_RankNormal_datarelease_12182019_", colnames(pheno)[14], "_", i, ".RData")))
  operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
}
operm <- matrix(do.call(rbind, operm[c(1:50)[c(-4,-8,-14,-15,-18,-28,-31)]]),ncol = 1)
class(operm) <- c("scan1perm", "matrix")
cutoff <- summary(operm, c(0.05, 0.1))[,1]

#genome-wide results
pdf(file = paste0("output/m2.69k.Novelty_residuals_RankNormal_datarelease_12182019", "_genomescan.pdf"), width = 14)
for(i in names(m2.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m2.qtl.out[[i]])*1.2 # overall maximum LOD score
  ymax <- ifelse(ymx > cutoff[1]*1.2, ymx, cutoff[1]*1.2)
  plot(m2.qtl.out[[i]], gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymax),
       main=i)
  abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()

png 
  2

#for(i in names(m2.qtl.out)){
#  par(mar=c(5.1, 4.1, 1.1, 1.1))
#  ymx <- maxlod(m2.qtl.out[[i]]) # overall maximum LOD score
#  plot(m2.qtl.out[[i]], gmap, lodcolumn=1,
#       col="slateblue", ylim=c(0, ymx*1.02),
#       main=i)
#  abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
#  abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
#}

#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
  y <- get(load(paste0("output/blup/m2_blup_69k_Novelty_residuals_RankNormal_datarelease_12182019_",i,".RData")))
  x[[i]] <- y[[i]]
}
m2.blup = x

#coeffects plot
pdf(file = paste0("output/m2.69k.Novelty_residuals_RankNormal_datarelease_12182019", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m2.qtl.out)){
  chr <- as.character(m2.peak[[i]][m2.peak[[i]]$lodcolumn == i,"chr"])
  par(mar=c(4.1, 4.1, 1.6, 1.6))
  #  plot_coefCC(m2.coef[[i]],
  #              gmap[chr],
  #              scan1_output=m2.qtl.out[[i]],
  #              bgcolor="gray95", #legend="bottomleft",
  #              main =i)
  plot_coefCC(m2.blup[[i]],
              gmap[chr],
              scan1_output=m2.qtl.out[[i]],
              bgcolor="gray95", #legend="bottomleft",
              main =i)
#   plot(m2.snps[[i]]$lod,
#        m2.snps[[i]]$snpinfo,
#        drop_hilit=1.5,
#        genes=m2.genes[[i]],
#        main = i)
}
dev.off()

png 
  2

for(i in names(m2.qtl.out)){
  print(i)
  if(is.null(m2.snps[[i]]))
    next

  if(dim(m2.genes[[i]]) == 0){
    m2.genes[[i]] = NA
  }

  top_1 <- data.frame(pheno = i)
  top <- top_snps(m2.snps[[i]]$lod, m2.snps[[i]]$snpinfo)
  top <- cbind(top_1, top)
  write.table(top, file = "output/Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", sep = ",",
              row.names = F, col.names = T, append = TRUE)
  
  topgene <- cbind(top_1, m2.genes[[i]])
  write.table(topgene, file = "output/Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", sep = ",",
              row.names = F, col.names = T, append = TRUE)
}

[1] "OFA.total.distance.traveled"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.distance.traveled.slope"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.time.in.corner"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.time.in.perimeter"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.time.in.center"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.ambulatory.time"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.distance.traveled.in.perimeter"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.distance.traveled.in.center"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.total.distance.traveled.in.corner"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.pct.dist.center"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.pct.dist.corner"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.pct.dist.perimeter"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.pct.time.center"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.pct.time.corner"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.pct.time.perimeter"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.distance.traveled.first.five"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "OFA.distance.traveled.last.five"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "LD.pct.distance.traveled.in.light"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "LD.pct.ambulatory.time.in.light"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "LD.pct.resting.time.in.light"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "LD.pct.time.in.light"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "LD.pct.ambulatory.Counts.in.light"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "LD.total.transitions"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "HB.Total.Entries"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "HB.Novel.Entries"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "HB.Repeat.Entries"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "NPP.NoveltyPreference.ZoneTime_WhiteVsBlack_Total"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

[1] "NPP.NoveltyPreference.ZoneTime_GreyWhiteBlack_Total"

Warning in if (dim(m2.genes[[i]]) == 0) {: the condition has length > 1 and
only the first element will be used

Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-variantlist.csv", :
appending column names to file

Warning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-69k-genelist.csv", :
appending column names to file

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

locale:
[1] C

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

other attached packages:
[1] ggplot2_3.1.0 qtl2_0.18    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        pillar_1.3.1      git2r_0.23.0     
 [4] plyr_1.8.4        workflowr_1.4.0   tools_3.3.2      
 [7] digest_0.6.18     bit_1.1-14        RSQLite_2.1.1    
[10] evaluate_0.10     memoise_1.1.0     tibble_2.1.3     
[13] gtable_0.2.0      pkgconfig_2.0.1   rlang_0.4.0      
[16] DBI_1.0.0         yaml_2.2.0        parallel_3.3.2   
[19] withr_2.1.2       stringr_1.3.1     dplyr_0.8.3      
[22] knitr_1.20        fs_1.2.6          rprojroot_1.3-2  
[25] bit64_0.9-7       grid_3.3.2        tidyselect_0.2.5 
[28] glue_1.3.1        data.table_1.11.4 R6_2.4.0         
[31] rmarkdown_1.11    purrr_0.3.2       blob_1.1.1       
[34] magrittr_1.5      whisker_0.3-2     backports_1.1.2  
[37] scales_1.0.0      htmltools_0.3.6   assertthat_0.2.1 
[40] colorspace_1.4-0  stringi_1.2.4     lazyeval_0.2.1   
[43] munsell_0.5.0     crayon_1.3.4

plot_qtl_69k_mapping_Novelty_residuals_RankNormal_datarelease_12182019

Hao He

2020-02-25

library

plot 69k scan result for m2 Novelty_residuals_RankNormal_datarelease_12182019