Plot_DO_morphine1_all_weight_age

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Last updated: 2020-09-15

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Knit directory: DO_Opioid/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Plot_DO_morphine1_all_weight_age.Rmd) and HTML (docs/Plot_DO_morphine1_all_weight_age.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
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html	7f32481	xhyuo	2020-09-15	Build site.
Rmd	40a36d7	xhyuo	2020-09-15	age

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Last update: 2020-09-15

loading libraries

library(qtl2)

rz.transform <- function(y) {
  rankY=rank(y, ties.method="average", na.last="keep")
  rzT=qnorm(rankY/(length(na.exclude(rankY))+1))
  return(rzT)
}
load("code/do.colors.RData")

Plot qtl mapping, First Batch

load("output/qtl.morphine.out.weight_age.RData")
load("output/do.morphine.RData")
#pmap and gmap
chr.names <- c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19", "X")
gmap <- list()
pmap <- list()
for (chr in chr.names){
  gmap[[chr]] <-  do.morphine$gmap[[chr]]
  pmap[[chr]] <-  do.morphine$pmap[[chr]]
}
attr(gmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)
attr(pmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)

#genome-wide plot
for(i in names(qtl.morphine.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(qtl.morphine.out[[i]]) # overall maximum LOD score
  plot(qtl.morphine.out[[i]], map=pmap, lodcolumn=1, col="slateblue", ylim=c(0, 10))
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[1]], col="red")
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[2]], col="red")
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[3]], col="red")
  title(main = paste0("DO_morphine_",i))
}

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#peaks coeff plot
for(i in names(qtl.morphine.out)){
  print(i)
  peaks <- find_peaks(qtl.morphine.out[[i]], map=pmap, threshold=6, drop=1.5)
  for(p in 1:dim(peaks)[1]) {
    print(p)
    chr <-peaks[p,3]
    #coeff plot
    par(mar=c(4.1, 4.1, 0.6, 0.6))
    # plot_coefCC(coef_c1[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
  }
}
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Plot qtl mapping, Second Batch

load("output/qtl.morphine.out.second_set.weight_age.RData")
do.morphine <- get(load("output/second_set_gm.RData"))
#pmap and gmap
chr.names <- c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19", "X")
gmap <- list()
pmap <- list()
for (chr in chr.names){
  gmap[[chr]] <-  do.morphine$gmap[[chr]]
  pmap[[chr]] <-  do.morphine$pmap[[chr]]
}
attr(gmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)
attr(pmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)

#genome-wide plot
for(i in names(qtl.morphine.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(qtl.morphine.out[[i]]) # overall maximum LOD score
  plot(qtl.morphine.out[[i]], map=pmap, lodcolumn=1, col="slateblue", ylim=c(0, 10))
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[1]], col="red")
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[2]], col="red")
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[3]], col="red")
  title(main = paste0("DO_morphine_",i))
}

Past versions of “Plot qtl mapping Second Batch-1.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Past versions of “Plot qtl mapping Second Batch-2.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Past versions of “Plot qtl mapping Second Batch-3.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Past versions of “Plot qtl mapping Second Batch-4.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

#peaks coeff plot
for(i in names(qtl.morphine.out)){
  print(i)
  peaks <- find_peaks(qtl.morphine.out[[i]], map=pmap, threshold=6, drop=1.5)
  for(p in 1:dim(peaks)[1]) {
    print(p)
    chr <-peaks[p,3]
    #coeff plot
    par(mar=c(4.1, 4.1, 0.6, 0.6))
    # plot_coefCC(coef_c1[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
  }
}
# [1] "Survival.Time"
# [1] 1

Past versions of “Plot qtl mapping Second Batch-5.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Second Batch-6.png”

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7f32481	xhyuo	2020-09-15

# [1] 3

Past versions of “Plot qtl mapping Second Batch-7.png”

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7f32481	xhyuo	2020-09-15

# [1] 4

Past versions of “Plot qtl mapping Second Batch-8.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] "Recovery.Time"
# [1] 1

Past versions of “Plot qtl mapping Second Batch-9.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Second Batch-10.png”

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7f32481	xhyuo	2020-09-15

# [1] 3

Past versions of “Plot qtl mapping Second Batch-11.png”

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7f32481	xhyuo	2020-09-15

# [1] "Min.depression"
# [1] 1

Past versions of “Plot qtl mapping Second Batch-12.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Second Batch-13.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] "Status_bin"
# [1] 1

Past versions of “Plot qtl mapping Second Batch-14.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Second Batch-15.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Plot qtl mapping, Combined

load("output/qtl.morphine.out.combined_weight_age.RData")
do.morphine <- get(load("output/second_set_gm.RData"))
#pmap and gmap
chr.names <- c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19", "X")
gmap <- list()
pmap <- list()
for (chr in chr.names){
  gmap[[chr]] <-  do.morphine$gmap[[chr]]
  pmap[[chr]] <-  do.morphine$pmap[[chr]]
}
attr(gmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)
attr(pmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)

#genome-wide plot
for(i in names(qtl.morphine.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(qtl.morphine.out[[i]]) # overall maximum LOD score
  plot(qtl.morphine.out[[i]], map=pmap, lodcolumn=1, col="slateblue", ylim=c(0, 10))
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[1]], col="red")
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[2]], col="red")
  abline(h=summary(qtl.morphine.operm[[i]], alpha=c(0.10, 0.05, 0.01))[[3]], col="red")
  title(main = paste0("DO_morphine_",i))
}

Past versions of “Plot qtl mapping Combined-1.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Past versions of “Plot qtl mapping Combined-2.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Past versions of “Plot qtl mapping Combined-3.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

Past versions of “Plot qtl mapping Combined-4.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

#peaks coeff plot
for(i in names(qtl.morphine.out)){
  print(i)
  peaks <- find_peaks(qtl.morphine.out[[i]], map=pmap, threshold=6, drop=1.5)
  for(p in 1:dim(peaks)[1]) {
    print(p)
    chr <-peaks[p,3]
    #coeff plot
    par(mar=c(4.1, 4.1, 0.6, 0.6))
    # plot_coefCC(coef_c1[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
  }
}
# [1] "Survival.Time"
# [1] 1

Past versions of “Plot qtl mapping Combined-5.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Combined-6.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 3

Past versions of “Plot qtl mapping Combined-7.png”

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7f32481	xhyuo	2020-09-15

# [1] "Recovery.Time"
# [1] 1

Past versions of “Plot qtl mapping Combined-8.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Combined-9.png”

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7f32481	xhyuo	2020-09-15

# [1] 3

Past versions of “Plot qtl mapping Combined-10.png”

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7f32481	xhyuo	2020-09-15

# [1] "Min.depression"
# [1] 1

Past versions of “Plot qtl mapping Combined-11.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] "Status_bin"
# [1] 1

Past versions of “Plot qtl mapping Combined-12.png”

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7f32481	xhyuo	2020-09-15

# [1] 2

Past versions of “Plot qtl mapping Combined-13.png”

Version	Author	Date
7f32481	xhyuo	2020-09-15

# [1] 3

Past versions of “Plot qtl mapping Combined-14.png”

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7f32481	xhyuo	2020-09-15

# [1] 4

Past versions of “Plot qtl mapping Combined-15.png”

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7f32481	xhyuo	2020-09-15

# [1] 5

Past versions of “Plot qtl mapping Combined-16.png”

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7f32481	xhyuo	2020-09-15

# [1] 6

Past versions of “Plot qtl mapping Combined-17.png”

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7f32481	xhyuo	2020-09-15

Session information

sessionInfo()
# R version 4.0.0 (2020-04-24)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 18.04.4 LTS
# 
# Matrix products: default
# BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.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=C             
#  [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] qtl2_0.22-8     workflowr_1.6.2
# 
# loaded via a namespace (and not attached):
#  [1] Rcpp_1.0.4.6      knitr_1.28        whisker_0.4       magrittr_1.5     
#  [5] bit_1.1-15.2      R6_2.4.1          rlang_0.4.6       blob_1.2.1       
#  [9] stringr_1.4.0     tools_4.0.0       parallel_4.0.0    data.table_1.12.8
# [13] xfun_0.13         DBI_1.1.0         git2r_0.27.1      htmltools_0.4.0  
# [17] yaml_2.2.1        bit64_0.9-7       digest_0.6.25     rprojroot_1.3-2  
# [21] later_1.0.0       vctrs_0.3.1       promises_1.1.0    fs_1.4.1         
# [25] memoise_1.1.0     glue_1.4.0        evaluate_0.14     RSQLite_2.2.0    
# [29] rmarkdown_2.3     stringi_1.4.6     compiler_4.0.0    backports_1.1.6  
# [33] httpuv_1.5.4

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