Plot_DO_Fentanyl_Cohort2_mapping

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Last updated: 2023-02-21

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Knit directory: DO_Opioid/

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Unstaged changes:
    Modified:   _workflowr.yml
    Modified:   analysis/marker_violin.Rmd

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 repository in which changes were made to the R Markdown (analysis/Plot_DO_Fentanyl_Cohort2_mapping.Rmd) and HTML (docs/Plot_DO_Fentanyl_Cohort2_mapping.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
Rmd	2200f95	xhyuo	2023-02-21	update with sex specific Fentanyl plot
html	8611541	xhyuo	2023-02-21	Build site.
Rmd	d1a7028	xhyuo	2023-02-21	update with sex specific Fentanyl
html	fd4dc88	xhyuo	2023-01-11	Build site.
Rmd	aff7cd2	xhyuo	2023-01-11	update with histogram
html	6eeaa6a	xhyuo	2023-01-06	Build site.
Rmd	6d89b79	xhyuo	2023-01-06	update with histogram and gcta h2, figure size
html	fe30eec	xhyuo	2023-01-06	Build site.
Rmd	15a2b6f	xhyuo	2023-01-06	update with histogram and gcta h2
html	b77b34e	xhyuo	2022-06-29	Build site.
Rmd	3f07442	xhyuo	2022-06-29	Plot_DO_Fentanyl_Cohort2
html	7faf7f1	xhyuo	2022-06-29	Build site.
Rmd	e9fb99f	xhyuo	2022-06-29	Fentanyl_Cohort2

---

Last update: 2023-02-21

loading libraries

library(ggplot2)
library(gridExtra)
library(GGally)
library(parallel)
library(qtl2)
library(parallel)
library(survival)
library(regress)
library(abind)
library(openxlsx)
library(tidyverse)

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")

Read phenotype data

# Read phenotype data -----------------------------------------------------
#batch 20220502
do.pheno <- readxl::read_excel(path = "data/Composite Post Kevins Program Group 2 Fentanyl Prepped for Hao.xlsx",
                                 col_types = c("text", "text", "text", "date", "numeric", "numeric", "date", rep("numeric", 9), "date"))
# Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
# Expecting date in D263 / R263C4: got 'BLANK'
# Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
# Expecting numeric in F263 / R263C6: got 'BLANK'
do.pheno <- do.pheno %>%
  dplyr::rename_with(., ~str_remove_all(.x, " ")) %>%
  dplyr::filter(!is.na(MouseID)) %>%
  dplyr::mutate(Status_bin = case_when(
    EarTag == "DEAD" ~ 0,
    is.na(EarTag) ~ 1
  )) %>%
  as.data.frame()

# Read genotype data -----------------------------------------------------------
load("data/Jackson_Lab_Bubier_MURGIGV01/gm_DO765_qc_newid.RData")#gm_after_qc
overlap.id  = intersect(ind_ids(gm_after_qc), as.character(do.pheno$MouseID))

#subset
gm = gm_after_qc[overlap.id, ]
do.pheno = do.pheno[do.pheno$MouseID %in% overlap.id, ]
rownames(do.pheno) = do.pheno$MouseID
do.pheno = do.pheno[overlap.id,]
all.equal(ind_ids(gm), do.pheno$MouseID)
# [1] TRUE

#covar
do.pheno$Sex <- as.factor(do.pheno$Sex)

#boxplot on the raw data------------
for(i in 8:16){
  df <- do.pheno[,c(1, 3, i)]
  df <- df[complete.cases(df), ]
  p <- ggplot(df, aes(x=Sex, y=df[,3], group = Sex, fill = Sex, alpha = 0.9)) + 
    geom_boxplot(show.legend = F , outlier.size = 1.5, notchwidth = 0.85) +
    geom_jitter(color="black", size=0.8, alpha=0.9) +
    scale_fill_brewer(palette="Blues") +
    ylab(paste0(colnames(df)[3])) +
    xlab("Sex") +
    labs(fill = "") +
    theme(legend.position = "none",
          panel.grid.major = element_blank(), 
          panel.grid.minor = element_blank(),
          panel.background = element_blank(), 
          axis.line = element_line(colour = "black"),
          text = element_text(size=21), 
          axis.title=element_text(size=21)) +
    guides(shape = guide_legend(override.aes = list(size = 12)))
  print(p)
}

Past versions of “Read phenotype data-1.png”

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fd4dc88	xhyuo	2023-01-11
fe30eec	xhyuo	2023-01-06

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fe30eec	xhyuo	2023-01-06

#histogram
for(i in c(8:10, 12:16)){
  df <- do.pheno[,c(1, 3, i)]
  p <- ggplot(data=df, aes(x=df[,3])) + 
  geom_histogram() +
  ylab("Number of DO mice") + 
  xlab(paste0(colnames(df)[3])) +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
                  panel.background = element_blank(), axis.line = element_line(colour = "black"),
                  text = element_text(size=21))
  print(p)
}
# Warning: Removed 132 rows containing non-finite values (stat_bin).

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fd4dc88	xhyuo	2023-01-11
fe30eec	xhyuo	2023-01-06

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#for "MinDepressionRR(%)"
i = 11
df <- do.pheno[,c(1, 3, i)]
p <- ggplot(data=df, aes(x=df[,3])) + 
geom_histogram() +
ylab("Number of DO mice") + 
xlab(paste0(colnames(df)[3])) +
xlim(0.4, 1) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
      panel.background = element_blank(), axis.line = element_line(colour = "black"),
      text = element_text(size=21))
print(p)
# Warning: Removed 48 rows containing non-finite values (stat_bin).
# Warning: Removed 2 rows containing missing values (geom_bar).

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fe30eec	xhyuo	2023-01-06

#boxplot on the rankz data------------
for(i in 8:16){
  df <- do.pheno[,c(1, 3, i)]
  df <- df[complete.cases(df), ]
  p <- ggplot(df, aes(x=Sex, y= rz.transform(df[,3]), group = Sex, fill = Sex, alpha = 0.9)) + 
    geom_boxplot(show.legend = F , outlier.size = 1.5, notchwidth = 0.85) +
    geom_jitter(color="black", size=0.8, alpha=0.9) +
    scale_fill_brewer(palette="Blues") +
    ylab(paste0("rz.transformed ", colnames(df)[3])) +
    xlab("Sex") +
    labs(fill = "") +
    theme(legend.position = "none",
          panel.grid.major = element_blank(), 
          panel.grid.minor = element_blank(),
          panel.background = element_blank(), 
          axis.line = element_line(colour = "black"),
          text = element_text(size=21), 
          axis.title=element_text(size=21)) +
    guides(shape = guide_legend(override.aes = list(size = 12)))
  print(p)
}

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#histogram
for(i in 8:16){
  df <- do.pheno[,c(1, 3, i)]
  p <- ggplot(data=df, aes(x=rz.transform(df[,3]))) + 
    geom_histogram() +
    ylab("Number of DO mice") + 
    xlab(paste0("rz.transformed ", colnames(df)[3])) +
    theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
          panel.background = element_blank(), axis.line = element_line(colour = "black"),
          text = element_text(size=21))
  print(p)
}
# Warning: Removed 132 rows containing non-finite values (stat_bin).

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fe30eec	xhyuo	2023-01-06

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Plot qtl mapping on array

Plot by using its output qtl.do_Fentanyl_Cohort2.out.RData

load("output/Fentanyl/qtl.do_Fentanyl_Cohort2.out.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]] <-  gm$gmap[[chr]]
  pmap[[chr]] <-  gm$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_Fentanyl_Cohort2_",i))
}

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

pdf(file = paste0("output/Fentanyl/do_Fentanyl_Cohort2.pdf"), width = 16, height =8)
#save genome-wide plo
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_Fentanyl_Cohort2_",i))
}
dev.off()
# png 
#   2
  
#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)
  if(nrow(peaks) > 0) {
    print(peaks)
    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=NULL)
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend=NULL)
    plot(out_snps[[i]][[p]]$lod, out_snps[[i]][[p]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[p]])
    }
  }
}
# [1] "TimetoDead(Hr)"
#   lodindex lodcolumn chr       pos      lod     ci_lo    ci_hi
# 1        1    pheno1   2 132.62489 7.067034 106.68530 133.3807
# 2        1    pheno1   3 100.24885 6.239943  80.21006 101.0701
# 3        1    pheno1   5  96.36969 6.019079  50.65575 147.9508
# 4        1    pheno1  13  91.52025 6.147871  48.80519 117.2887
# [1] 1

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 2

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 3

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

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-18.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-19.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 4

Past versions of “Plot qtl mapping on array-20.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-21.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-22.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "RRDepressionRate(%/Hr)SLOPE"
# [1] "TimetoSteadyRRDepression(Hr)"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   5 120.68390 6.483622 118.27549 121.58096
# 2        1    pheno1  17  52.79771 7.779978  52.16947  53.54382
# 3        1    pheno1  18  63.05026 6.127351  49.68747  63.25613
# [1] 1

Past versions of “Plot qtl mapping on array-23.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-24.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-25.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 2

Past versions of “Plot qtl mapping on array-26.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-27.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-28.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 3

Past versions of “Plot qtl mapping on array-29.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-30.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-31.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "MinDepressionRR(%)"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1   8 14.56268 6.752336 14.38322 14.60657
# [1] 1

Past versions of “Plot qtl mapping on array-32.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-33.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-34.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "Steady-StateDepressionDuration(Hr)INTERVAL"
# [1] "TimetoThresholdRecovery(Hr)"
#   lodindex lodcolumn chr      pos      lod    ci_lo     ci_hi
# 1        1    pheno1   1 91.31201 6.658992 91.21626 153.19382
# 2        1    pheno1   8 92.31720 6.295785 14.56005 109.54470
# 3        1    pheno1  13 53.62165 7.712830 53.57538  54.08557
# 4        1    pheno1  15 89.24166 6.222582 60.56487  90.52322
# [1] 1

Past versions of “Plot qtl mapping on array-35.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-36.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-37.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 2

Past versions of “Plot qtl mapping on array-38.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-39.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-40.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 3

Past versions of “Plot qtl mapping on array-41.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-42.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-43.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 4

Past versions of “Plot qtl mapping on array-44.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-45.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-46.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "TimetoProjectedRecovery(Hr)"
#   lodindex lodcolumn chr       pos      lod    ci_lo     ci_hi
# 1        1    pheno1   1 152.43451 6.138085 91.21626 153.19382
# 2        1    pheno1   8  92.31720 6.032551 14.55032  92.73082
# 3        1    pheno1  13  53.62165 6.969155 53.57538  53.97165
# 4        1    pheno1  18  66.14084 6.606701 65.31382  66.30142
# [1] 1

Past versions of “Plot qtl mapping on array-47.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-48.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-49.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 2

Past versions of “Plot qtl mapping on array-50.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-51.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-52.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 3

Past versions of “Plot qtl mapping on array-53.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-54.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-55.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 4

Past versions of “Plot qtl mapping on array-56.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-57.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-58.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "StartofRecovery(Hr)"
#   lodindex lodcolumn chr      pos     lod    ci_lo    ci_hi
# 1        1    pheno1  13 53.62165 6.12149 53.57538 54.62068
# [1] 1

Past versions of “Plot qtl mapping on array-59.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-60.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-61.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "RRRecoveryRate(%/Hr)SLOPE"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   6 115.70560 6.308902 115.43247 116.28985
# 2        1    pheno1  10  68.11376 6.195341  66.55149  68.20195
# 3        1    pheno1  15  90.42378 6.347611  88.92565  90.85895
# 4        1    pheno1  18  65.52797 6.640763  65.36123  65.58896
# [1] 1

Past versions of “Plot qtl mapping on array-62.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-63.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-64.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 2

Past versions of “Plot qtl mapping on array-65.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-66.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-67.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 3

Past versions of “Plot qtl mapping on array-68.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-69.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-70.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] 4

Past versions of “Plot qtl mapping on array-71.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-72.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-73.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

# [1] "Status_bin"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1  11 56.51261 6.370706 28.86938 56.80903
# [1] 1

Past versions of “Plot qtl mapping on array-74.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-75.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

Past versions of “Plot qtl mapping on array-76.png”

Version	Author	Date
7faf7f1	xhyuo	2022-06-29

#save 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)
  if(nrow(peaks) > 0){
      fname <- paste("output/DO_Fentanyl_Cohort2_", str_replace_all(i, "[[:punct:]]", "") ,"_coefplot.pdf",sep="")
      pdf(file = fname, width = 16, height =8)
      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=NULL)
        plot(out_snps[[i]][[p]]$lod, out_snps[[i]][[p]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[p]])
        }
      dev.off()
  }
}
# [1] "TimetoDead(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "RRDepressionRate(%/Hr)SLOPE"
# [1] "TimetoSteadyRRDepression(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] "MinDepressionRR(%)"
# [1] 1
# [1] "Steady-StateDepressionDuration(Hr)INTERVAL"
# [1] "TimetoThresholdRecovery(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "TimetoProjectedRecovery(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "StartofRecovery(Hr)"
# [1] 1
# [1] "RRRecoveryRate(%/Hr)SLOPE"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "Status_bin"
# [1] 1

#save peaks coeff blup plot
for(i in names(qtl.morphine.out)){
  print(i)
  peaks <- find_peaks(qtl.morphine.out[[i]], map=pmap, threshold=6, drop=1.5)
  if(nrow(peaks) > 0) {
      fname <- paste("output/DO_Fentanyl_Cohort2_", str_replace_all(i, "[[:punct:]]", "") ,"_coefplot_blup.pdf",sep="")
      pdf(file = fname, width = 16, height =8)
      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_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend=NULL)
        plot(out_snps[[i]][[p]]$lod, out_snps[[i]][[p]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[p]])
        }
      dev.off()
    }
}
# [1] "TimetoDead(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "RRDepressionRate(%/Hr)SLOPE"
# [1] "TimetoSteadyRRDepression(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] "MinDepressionRR(%)"
# [1] 1
# [1] "Steady-StateDepressionDuration(Hr)INTERVAL"
# [1] "TimetoThresholdRecovery(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "TimetoProjectedRecovery(Hr)"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "StartofRecovery(Hr)"
# [1] 1
# [1] "RRRecoveryRate(%/Hr)SLOPE"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] "Status_bin"
# [1] 1

heritability

#plot heritability by qtl2 array --------------
herit <- data.frame(Phenotype = names(unlist(qtl.morphine.hsq)),
                    Heritability = round(unlist(qtl.morphine.hsq),3))
herit <- herit %>%
  arrange(desc(Heritability))
herit$Phenotype <- factor(herit$Phenotype, levels = herit$Phenotype)
#histgram
p2 <- ggplot(data=herit, aes(x=Phenotype, y=Heritability)) + #, fill=Domain, color = Domain)) +
  geom_bar(stat="identity", fill = "blue", color = "blue", show.legend = FALSE) +
  scale_y_continuous(breaks=seq(0.0, 1.0, 0.1)) +
  geom_text(aes(label = Heritability, y = Heritability + 0.005), position = position_dodge(0.9),vjust = 0) +
  theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
  ggtitle("DO Fentanyl_Cohort2 Heritability by qtl2 array")
p2

Past versions of heritability-1.png

Version	Author	Date
6eeaa6a	xhyuo	2023-01-06
7faf7f1	xhyuo	2022-06-29

#plot heritability by GCTA
h <- read.csv("data/FinalReport/GCTA/DO_Fentanyl_Cohort2/DO_Fentanyl_Cohort2_heritability_by_GCTA.csv", header = TRUE)
h <- h %>%
  arrange(desc(Heritability))
h$Phenotype <- factor(h$Phenotype, levels = h$Phenotype)
h$Heritability <- round(h$Heritability,2)
#histgram
pdf(file = paste0("data/FinalReport/GCTA/DO_Fentanyl_Cohort2/DO_Fentanyl_Cohort2","_heritability_by_GCTA.pdf"), height = 10, width = 10)
p3<-ggplot(data=h, aes(x=Phenotype, y=Heritability)) + #, fill=Domain, color = Domain)) +
  geom_bar(stat="identity", fill = "blue", color = "blue", show.legend = FALSE) +
  scale_y_continuous(breaks=seq(0.0, 1.0, 0.1)) +
  geom_text(aes(label = Heritability, y = Heritability + 0.005), position = position_dodge(0.9),vjust = 0) +
  theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
  ggtitle("Heritability by GCTA")
p3
dev.off()
# png 
#   2
# png 
#   2
p3

Past versions of heritability-2.png

Version	Author	Date
6eeaa6a	xhyuo	2023-01-06
fe30eec	xhyuo	2023-01-06

Plot qtl mapping on array male

load("output/Fentanyl/qtl.do_Fentanyl_Cohort2.out.male.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]] <-  gm$gmap[[chr]]
  pmap[[chr]] <-  gm$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, max(sapply(qtl.morphine.out, maxlod)) +2))
  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_Fentanyl_Cohort2_",i))
}

Past versions of “Plot qtl mapping on array male-1.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-2.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-3.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-4.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-5.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-6.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-7.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-8.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-9.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-10.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

  
#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)
  if(nrow(peaks) > 0) {
    print(peaks)
    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=NULL)
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend=NULL)
    plot(out_snps[[i]][[p]]$lod, out_snps[[i]][[p]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[p]])
    }
  }
}
# [1] "TimetoDead(Hr)"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   2 132.62489 8.135472 131.88985 132.94007
# 2        1    pheno1   3  80.46385 6.635020  73.35207  81.19227
# 3        1    pheno1   5  13.42743 6.684415  10.86410  14.21411
# 4        1    pheno1   9  13.71424 6.527954  13.12685  15.44563
# [1] 1

Past versions of “Plot qtl mapping on array male-11.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-12.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-13.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-14.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-15.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-16.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array male-17.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-18.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-19.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array male-20.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-21.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-22.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "RRDepressionRate(%/Hr)SLOPE"
#   lodindex lodcolumn chr      pos      lod     ci_lo    ci_hi
# 1        1    pheno1   3 32.58987 6.984733 32.379800 33.07485
# 2        1    pheno1   X 10.46006 7.122931  9.261486 53.15896
# [1] 1

Past versions of “Plot qtl mapping on array male-23.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-24.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-25.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-26.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-27.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-28.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "TimetoSteadyRRDepression(Hr)"
#   lodindex lodcolumn chr      pos      lod    ci_lo     ci_hi
# 1        1    pheno1   2 161.6875 6.026396 95.37519 161.87139
# 2        1    pheno1  17  52.1811 6.074600 36.63825  53.54382
# [1] 1

Past versions of “Plot qtl mapping on array male-29.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-30.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-31.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-32.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-33.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-34.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "MinDepressionRR(%)"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   2 168.30118 6.308975 167.55191 171.64499
# 2        1    pheno1  13  89.64923 6.299108  52.44224  90.31856
# [1] 1

Past versions of “Plot qtl mapping on array male-35.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-36.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-37.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-38.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-39.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-40.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "Steady-StateDepressionDuration(Hr)INTERVAL"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   3  90.66061 8.142433  90.57609  90.70492
# 2        1    pheno1   4 100.75953 7.510841  99.32926 100.79381
# 3        1    pheno1   8  83.45834 6.695546  83.35490  84.22023
# 4        1    pheno1   9 123.42827 6.428620 116.93394 123.85184
# 5        1    pheno1  10  66.55650 6.997621  64.45014  69.65303
# 6        1    pheno1  12  75.98747 7.912513  75.95610  94.21761
# 7        1    pheno1  13  93.91029 6.097764  42.38805  95.63661
# [1] 1

Past versions of “Plot qtl mapping on array male-41.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-42.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-43.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-44.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-45.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-46.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array male-47.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-48.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-49.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array male-50.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-51.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-52.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array male-53.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-54.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-55.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 6

Past versions of “Plot qtl mapping on array male-56.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-57.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-58.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 7

Past versions of “Plot qtl mapping on array male-59.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-60.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-61.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "TimetoThresholdRecovery(Hr)"
#   lodindex lodcolumn chr      pos      lod    ci_lo     ci_hi
# 1        1    pheno1   2 80.18535 6.172261 65.91339 181.81225
# 2        1    pheno1  12 75.98747 7.498411 75.94321  75.99396
# [1] 1

Past versions of “Plot qtl mapping on array male-62.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-63.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-64.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-65.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-66.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-67.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "TimetoProjectedRecovery(Hr)"
#   lodindex lodcolumn chr       pos      lod    ci_lo     ci_hi
# 1        1    pheno1   2  80.18535 6.137005 65.91339 180.94469
# 2        1    pheno1   3  90.66241 7.109982 89.60391 104.52824
# 3        1    pheno1   4  14.49143 6.166787 13.87348 153.99966
# 4        1    pheno1   6 110.87154 6.105875 23.39815 111.51060
# 5        1    pheno1  10  66.55650 6.203671 33.86040  67.04043
# 6        1    pheno1  12  91.62691 6.136398 75.62742  94.37674
# 7        1    pheno1  15  83.10382 6.748883 83.06880  83.13036
# [1] 1

Past versions of “Plot qtl mapping on array male-68.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-69.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-70.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-71.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-72.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-73.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array male-74.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-75.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-76.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array male-77.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-78.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-79.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array male-80.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-81.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-82.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 6

Past versions of “Plot qtl mapping on array male-83.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-84.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-85.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 7

Past versions of “Plot qtl mapping on array male-86.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-87.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-88.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "StartofRecovery(Hr)"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   3  90.66061 8.542034  90.57609  90.70492
# 2        1    pheno1   4 100.55380 7.820399  99.32926 100.79381
# 3        1    pheno1   8  83.45834 6.600689  70.15607  84.22023
# 4        1    pheno1   9 123.42827 6.126531 116.90024 123.85184
# 5        1    pheno1  10  65.71837 7.117583  64.45014  66.60381
# 6        1    pheno1  12  75.98747 8.039338  75.95610  94.18281
# 7        1    pheno1  13  95.62986 6.411262  43.57533  95.63661
# [1] 1

Past versions of “Plot qtl mapping on array male-89.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-90.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-91.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-92.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-93.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-94.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array male-95.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-96.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-97.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array male-98.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-99.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-100.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array male-101.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-102.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-103.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 6

Past versions of “Plot qtl mapping on array male-104.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-105.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-106.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 7

Past versions of “Plot qtl mapping on array male-107.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-108.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-109.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "RRRecoveryRate(%/Hr)SLOPE"
#   lodindex lodcolumn chr       pos      lod      ci_lo     ci_hi
# 1        1    pheno1   1 192.12423 6.708234 191.931595 193.43806
# 2        1    pheno1   2  30.42672 7.319624  30.269862  30.50527
# 3        1    pheno1   3 152.71526 6.460920  50.440226 153.14209
# 4        1    pheno1   9  54.54239 6.189928   6.239837  55.29730
# 5        1    pheno1  15  87.57068 6.600476  84.049458  90.51963
# [1] 1

Past versions of “Plot qtl mapping on array male-110.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-111.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-112.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-113.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-114.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-115.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array male-116.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-117.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-118.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array male-119.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-120.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-121.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array male-122.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-123.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-124.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "Status_bin"
#   lodindex lodcolumn chr      pos      lod    ci_lo     ci_hi
# 1        1    pheno1   7 49.25215 9.875931 46.83042  49.37829
# 2        1    pheno1   9 53.68682 6.144273 52.14281 119.66040
# 3        1    pheno1  19 53.55175 6.642364 53.11032  53.65224
# [1] 1

Past versions of “Plot qtl mapping on array male-125.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-126.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-127.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array male-128.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-129.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-130.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array male-131.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-132.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array male-133.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Plot qtl mapping on array female

load("output/Fentanyl/qtl.do_Fentanyl_Cohort2.out.female.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]] <-  gm$gmap[[chr]]
  pmap[[chr]] <-  gm$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, max(sapply(qtl.morphine.out, maxlod)) +2))
  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_Fentanyl_Cohort2_",i))
}

Past versions of “Plot qtl mapping on array female-1.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-2.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-3.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-4.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-5.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-6.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-7.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-8.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-9.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-10.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

  
#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)
  if(nrow(peaks) > 0) {
    print(peaks)
    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=NULL)
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend=NULL)
    plot(out_snps[[i]][[p]]$lod, out_snps[[i]][[p]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[p]])
    }
  }
}
# [1] "TimetoDead(Hr)"
#   lodindex lodcolumn chr      pos      lod    ci_lo     ci_hi
# 1        1    pheno1   2 35.93828 6.395693 14.71230  53.73635
# 2        1    pheno1   7 29.33386 7.380186 28.72162 107.32907
# 3        1    pheno1   9 29.84406 6.460520 28.55111  64.47467
# 4        1    pheno1  10 93.92129 6.138204 26.38250  94.50163
# 5        1    pheno1   X 45.99921 6.955609 44.92816 136.45503
# [1] 1

Past versions of “Plot qtl mapping on array female-11.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-12.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-13.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-14.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-15.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-16.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-17.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-18.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-19.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array female-20.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-21.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-22.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array female-23.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-24.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-25.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "RRDepressionRate(%/Hr)SLOPE"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   5  34.10212 6.494372  33.30631  34.38771
# 2        1    pheno1  12 110.17735 7.475173 109.51204 112.34613
# 3        1    pheno1  15  99.39531 6.125827  26.44955 101.12575
# [1] 1

Past versions of “Plot qtl mapping on array female-26.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-27.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-28.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-29.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-30.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-31.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-32.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-33.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-34.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "TimetoSteadyRRDepression(Hr)"
# [1] "MinDepressionRR(%)"
#   lodindex lodcolumn chr       pos      lod    ci_lo     ci_hi
# 1        1    pheno1   5 147.27839 6.273736 67.23641 147.43417
# 2        1    pheno1   6  52.83155 6.076547 13.21830  53.95921
# 3        1    pheno1  12 110.14878 6.256748 90.07443 110.17562
# 4        1    pheno1  18  41.80133 6.871462 41.74898  43.29028
# [1] 1

Past versions of “Plot qtl mapping on array female-35.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-36.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-37.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-38.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-39.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-40.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-41.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-42.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-43.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array female-44.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-45.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-46.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "Steady-StateDepressionDuration(Hr)INTERVAL"
#   lodindex lodcolumn chr        pos      lod      ci_lo     ci_hi
# 1        1    pheno1   6 126.017905 6.048217 125.696341 136.70757
# 2        1    pheno1   8  92.203842 6.030778  16.080653 124.33745
# 3        1    pheno1  10   5.635019 6.925830   3.400722 115.81149
# 4        1    pheno1  18  65.434900 6.977069  65.313821  65.52767
# [1] 1

Past versions of “Plot qtl mapping on array female-47.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-48.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-49.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-50.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-51.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-52.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-53.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-54.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-55.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array female-56.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-57.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-58.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "TimetoThresholdRecovery(Hr)"
#   lodindex lodcolumn chr        pos      lod      ci_lo     ci_hi
# 1        1    pheno1   1  91.312012 6.278565  91.216258 152.86541
# 2        1    pheno1   6 126.017905 6.903066 125.696341 126.63864
# 3        1    pheno1  10   5.635019 6.436675   3.174515 115.81149
# 4        1    pheno1  18  65.438329 7.680994  65.313821  65.52797
# [1] 1

Past versions of “Plot qtl mapping on array female-59.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-60.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-61.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-62.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-63.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-64.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-65.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-66.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-67.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array female-68.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-69.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-70.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "TimetoProjectedRecovery(Hr)"
#   lodindex lodcolumn chr       pos      lod      ci_lo     ci_hi
# 1        1    pheno1   1  91.31201 6.270337  91.209902 152.86541
# 2        1    pheno1   6 126.01790 6.709756 125.696341 126.61414
# 3        1    pheno1  10 115.79817 6.081346   3.174515 115.81494
# 4        1    pheno1  11  35.91853 6.293340  35.844802  35.99807
# 5        1    pheno1  18  65.43490 7.710831  65.313821  65.52767
# [1] 1

Past versions of “Plot qtl mapping on array female-71.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-72.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-73.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-74.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-75.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-76.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-77.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-78.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-79.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array female-80.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-81.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-82.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array female-83.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-84.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-85.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "StartofRecovery(Hr)"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1  10  5.635019 6.852134  3.400722 115.81149
# 2        1    pheno1  18 65.434900 6.749689 65.313821  65.52767
# [1] 1

Past versions of “Plot qtl mapping on array female-86.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-87.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-88.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-89.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-90.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-91.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "RRRecoveryRate(%/Hr)SLOPE"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   4 152.69816 6.100750  68.40926 152.83582
# 2        1    pheno1   5  13.65223 6.943854  13.42743  54.23998
# 3        1    pheno1   9 122.67218 7.020565 122.31448 123.93203
# 4        1    pheno1  12 113.10511 6.093534 112.53083 113.14986
# 5        1    pheno1  16  33.09290 7.445865  32.54616  92.27653
# [1] 1

Past versions of “Plot qtl mapping on array female-92.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-93.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-94.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 2

Past versions of “Plot qtl mapping on array female-95.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-96.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-97.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 3

Past versions of “Plot qtl mapping on array female-98.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-99.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-100.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 4

Past versions of “Plot qtl mapping on array female-101.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-102.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-103.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] 5

Past versions of “Plot qtl mapping on array female-104.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-105.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-106.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

# [1] "Status_bin"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1   1 149.3413 6.686633 145.0415 150.4074
# [1] 1

Past versions of “Plot qtl mapping on array female-107.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-108.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Past versions of “Plot qtl mapping on array female-109.png”

Version	Author	Date
8611541	xhyuo	2023-02-21

Session information

sessionInfo()
# R version 4.0.3 (2020-10-10)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 20.04.2 LTS
# 
# Matrix products: default
# BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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] parallel  stats     graphics  grDevices utils     datasets  methods  
# [8] base     
# 
# other attached packages:
#  [1] forcats_0.5.1   stringr_1.4.0   dplyr_1.0.4     purrr_0.3.4    
#  [5] readr_1.4.0     tidyr_1.1.2     tibble_3.0.6    tidyverse_1.3.0
#  [9] openxlsx_4.2.3  abind_1.4-5     regress_1.3-21  survival_3.2-7 
# [13] qtl2_0.24       GGally_2.1.0    gridExtra_2.3   ggplot2_3.3.3  
# [17] workflowr_1.6.2
# 
# loaded via a namespace (and not attached):
#  [1] httr_1.4.2         bit64_4.0.5        jsonlite_1.7.2     splines_4.0.3     
#  [5] modelr_0.1.8       assertthat_0.2.1   highr_0.8          blob_1.2.1        
#  [9] cellranger_1.1.0   yaml_2.2.1         pillar_1.4.7       RSQLite_2.2.3     
# [13] backports_1.2.1    lattice_0.20-41    glue_1.4.2         digest_0.6.27     
# [17] RColorBrewer_1.1-2 promises_1.2.0.1   rvest_0.3.6        colorspace_2.0-0  
# [21] htmltools_0.5.1.1  httpuv_1.5.5       Matrix_1.3-2       plyr_1.8.6        
# [25] pkgconfig_2.0.3    broom_0.7.4        haven_2.3.1        scales_1.1.1      
# [29] whisker_0.4        later_1.1.0.1      git2r_0.28.0       farver_2.0.3      
# [33] generics_0.1.0     ellipsis_0.3.1     cachem_1.0.4       withr_2.4.1       
# [37] cli_2.3.0          magrittr_2.0.1     crayon_1.4.1       readxl_1.3.1      
# [41] memoise_2.0.0      evaluate_0.14      fs_1.5.0           xml2_1.3.2        
# [45] tools_4.0.3        data.table_1.13.6  hms_1.0.0          lifecycle_1.0.0   
# [49] reprex_1.0.0       munsell_0.5.0      zip_2.1.1          compiler_4.0.3    
# [53] rlang_1.0.2        grid_4.0.3         rstudioapi_0.13    labeling_0.4.2    
# [57] rmarkdown_2.6      gtable_0.3.0       DBI_1.1.1          reshape_0.8.8     
# [61] R6_2.5.0           lubridate_1.7.9.2  knitr_1.31         fastmap_1.1.0     
# [65] bit_4.0.4          rprojroot_2.0.2    stringi_1.5.3      Rcpp_1.0.6        
# [69] vctrs_0.3.6        dbplyr_2.1.0       tidyselect_1.1.0   xfun_0.21

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