Plot_DO_morphine_secondbatch

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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/Plot_DO_Fentanyl_Cohort2_mapping.Rmd
    Modified:   analysis/Plot_DO_Fentanyl_combining2Cohort_mapping.Rmd
    Modified:   analysis/Plot_DO_fentanyl.Rmd
    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_morphine_combined.Rmd) and HTML (docs/Plot_DO_morphine_combined.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	cc3ae27	xhyuo	2023-02-21	update with sex specific morphine plot
html	8fe8543	xhyuo	2023-02-20	Build site.
Rmd	b46775c	xhyuo	2023-02-20	update with sex specific morphine
html	422da68	xhyuo	2020-07-12	Build site.
Rmd	f210d8a	xhyuo	2020-07-12	Plot_DO_morphine_combined

---

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("readxl")

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 for first batch-----------------------------------------------------
#morphine pheno
morphine.pheno <- read.csv("data/pheno_qtl2_07092018_morphine.csv",header = T)
#remove duplicate id
morphine.pheno <- morphine.pheno[!morphine.pheno$X %in% c("morphine_DO_jbubier_13645_C9", "morphine_DO_jbubier_13554_H1"),]
morphine.pheno <- data.frame(ID = morphine.pheno$X,
                             Sex = NA,
                             GENERATION = NA,
                             GROUP = NA,
                             Date = NA,
                             Status24 = morphine.pheno$Status,
                             Survival.Time = morphine.pheno$Survival.Time,
                             Recovery.Time = morphine.pheno$Recovery.Time,
                             Min.depression = morphine.pheno$Min.depression,
                             Status_bin = morphine.pheno$Status_bin,
                             RL = "NO")
rownames(morphine.pheno) <- gsub("morphine_DO_jbubier_","", morphine.pheno$ID)
rownames(morphine.pheno) <- gsub("\\_.*","", rownames(morphine.pheno))

# Read phenotype data for second batch-----------------------------------------------------
second_set <- read_xlsx(path = "data/MasterMorphine Second Set DO.xlsx",
                        sheet = 1)
second_set <- as.data.frame(second_set)
colnames(second_set)[2] <- "Sex"
colnames(second_set)[6] <- "Status24"
#character
second_set[,c("ID", "Sex", "GROUP", "Status24")] <- lapply(second_set[, c("ID", "Sex", "GROUP", "Status24")], as.character)
second_set$Status_bin <- ifelse(second_set$Status24 == "ALIVE", 1, 0)
rownames(second_set) <- second_set$ID

#remove outlier
second_set <- second_set[second_set$ID != "empty",]
colnames(second_set) <- c("ID","Sex","GENERATION","GROUP","Date",
                          "Status24", "Survival.Time","Recovery.Time", "Min.depression",
                          "Status_bin")
#remove negative survival time subjects
second_set <- second_set[!(!is.na(second_set$Survival.Time) & second_set$Survival.Time < 0),]
second_set$Survival.Time[!is.na(second_set$Survival.Time) & second_set$Survival.Time > 15] <- NA
second_set$Recovery.Time[!is.na(second_set$Recovery.Time) & second_set$Recovery.Time > 24] <- NA
second_set$Min.depression[!is.na(second_set$Min.depression) & second_set$Min.depression > 1] <- NA
second_set$RL = "YES"

#combined pheno
pheno <- rbind(morphine.pheno, second_set)

#load json object
load("/projects/csna/csna_workflow/data/Jackson_Lab_11_batches/gm_DO2816_qc.RData")
#replace id names
old_ids <- paste0(as.character(do.call(rbind.data.frame, strsplit(ind_ids(gm_DO2816_qc), "_"))[,6]))
old_ids <- make.unique(as.character(old_ids), sep = "_")
new_ids <- setNames(old_ids,
                    ind_ids(gm_DO2816_qc))
combined_gm <- replace_ids(gm_DO2816_qc, new_ids)[intersect(rownames(pheno),old_ids), ]
combined_gm
# Object of class cross2 (crosstype "do")
# 
# Total individuals               646
# No. genotyped individuals       646
# No. phenotyped individuals      646
# No. with both geno & pheno      646
# 
# No. phenotypes                    1
# No. covariates                    4
# No. phenotype covariates          0
# 
# No. chromosomes                  20
# Total markers                112455
# 
# No. markers by chr:
#    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
# 8530 8649 6403 6600 6559 6427 6281 5660 5854 5439 6338 5151 5257 5025 4547 4355 
#   17   18   19    X 
# 4321 3986 3102 3971

#update pheno
pheno <- merge(pheno, combined_gm$covar, by = "row.names", all.y = "TRUE")
rownames(pheno) <- pheno$Row.names
pheno <- pheno[,-1]
#remove generation 32 35
pheno <- pheno[!pheno$ngen %in% c("32", "35"),]

combined_gm <- combined_gm[rownames(pheno),]
combined_gm
# Object of class cross2 (crosstype "do")
# 
# Total individuals               637
# No. genotyped individuals       637
# No. phenotyped individuals      637
# No. with both geno & pheno      637
# 
# No. phenotypes                    1
# No. covariates                    4
# No. phenotype covariates          0
# 
# No. chromosomes                  20
# Total markers                112455
# 
# No. markers by chr:
#    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
# 8530 8649 6403 6600 6559 6427 6281 5660 5854 5439 6338 5151 5257 5025 4547 4355 
#   17   18   19    X 
# 4321 3986 3102 3971

#covar
#first batch
covar1 <- read.csv("data/GM_covar_07092018_morphine.csv",header = T)
#remove duplicate id
covar1 <- covar1[!covar1$X %in% c("morphine_DO_jbubier_13645_C9", "morphine_DO_jbubier_13554_H1"),]
rownames(covar1) <- gsub("morphine_DO_jbubier_","", covar1$id)
rownames(covar1) <- gsub("\\_.*","", rownames(covar1))
covar1 <- covar1[,c(2:5)]
colnames(covar1) <- c("ID", "Sex", "GENERATION", "Date")

#second batch
covar2 <- second_set[,c("ID", "Sex", "GENERATION", "Date")]
covar2$Date <- as.character(covar2$Date)

#combine covar
covar <- rbind(covar1, covar2)
covar <- covar[rownames(pheno),]
covar$Sex <- as.factor(covar$Sex)
covar$Date <- as.factor(covar$Date)

all.equal(rownames(pheno), rownames(covar))
# [1] TRUE

#boxplot for the pheno by generation
data <- cbind(pheno, covar)
#boxplot
#survival time
surv <- data[,c(1, 7, 11, 14, 15, 19)]
surv$ngen <- factor(surv$ngen, levels = as.character(c(29:34)))
p1 <- ggplot(surv, aes(x=ngen, y=Survival.Time, group = ngen, fill = ngen, 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("Survival Time") +
  xlab("Generation") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p1
# Warning: Removed 384 rows containing non-finite values (stat_boxplot).
# Warning: Removed 384 rows containing missing values (geom_point).

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

p1.1 <- ggplot(surv, aes(x=sex, y=Survival.Time, 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("Survival Time") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p1.1
# Warning: Removed 384 rows containing non-finite values (stat_boxplot).

# Warning: Removed 384 rows containing missing values (geom_point).

Past versions of “Read phenotype data-2.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

p1.2 <- ggplot(surv, aes(x=RL, y=Survival.Time, group = RL, fill = RL, 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("Survival Time") +
  xlab("RL") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p1.2
# Warning: Removed 384 rows containing non-finite values (stat_boxplot).

# Warning: Removed 384 rows containing missing values (geom_point).

Past versions of “Read phenotype data-3.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

reco <- data[,c(1, 8, 11, 14, 15, 19)]
reco$ngen <- factor(reco$ngen, levels = as.character(c(29:35)))
p2 <- ggplot(reco, aes(x=ngen, y=Recovery.Time, group = ngen, fill = ngen, 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("Recovery Time") +
  xlab("Generation") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p2
# Warning: Removed 266 rows containing non-finite values (stat_boxplot).
# Warning: Removed 266 rows containing missing values (geom_point).

Past versions of “Read phenotype data-4.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

p2.1 <- ggplot(reco, aes(x=sex, y=Recovery.Time, 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("Recovery Time") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p2.1
# Warning: Removed 266 rows containing non-finite values (stat_boxplot).

# Warning: Removed 266 rows containing missing values (geom_point).

Past versions of “Read phenotype data-5.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

p2.2 <- ggplot(reco, aes(x=RL, y=Recovery.Time, group = RL, fill = RL, 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("Recovery Time") +
  xlab("RL") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p2.2
# Warning: Removed 266 rows containing non-finite values (stat_boxplot).

# Warning: Removed 266 rows containing missing values (geom_point).

Past versions of “Read phenotype data-6.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

dep <- data[,c(1, 9, 11, 14, 15, 19)]
dep$ngen <- factor(dep$ngen, levels = as.character(c(29:35)))
p3 <- ggplot(dep, aes(x=ngen, y=Min.depression, group = ngen, fill = ngen, 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("Min depression") +
  xlab("Generation") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p3
# Warning: Removed 41 rows containing non-finite values (stat_boxplot).
# Warning: Removed 41 rows containing missing values (geom_point).

Past versions of “Read phenotype data-7.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

p3.1 <- ggplot(dep, aes(x=sex, y=Min.depression, 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("Min depression") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p3.1
# Warning: Removed 41 rows containing non-finite values (stat_boxplot).

# Warning: Removed 41 rows containing missing values (geom_point).

Past versions of “Read phenotype data-8.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

p3.2 <- ggplot(dep, aes(x=RL, y=Min.depression, group = RL, fill = RL, 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("Min depression") +
  xlab("RL") +
  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=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p3.2
# Warning: Removed 41 rows containing non-finite values (stat_boxplot).

# Warning: Removed 41 rows containing missing values (geom_point).

Past versions of “Read phenotype data-9.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Plot qtl mapping on 69k

Plot by using its output qtl.morphine.69k.out.combined.RData

load("output/qtl.morphine.69k.out.combined.RData")
#pmap and gmap
load("data/69k_grid_pgmap.RData")

#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 on 69k-1.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-2.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-3.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-4.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

#save genome-wide plot
for(i in names(qtl.morphine.out)){
  png(file = paste0("output/DO_morphine_secondbatch_", i, ".png"), width = 16, height =8, res=300, units = "in")
  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))
  dev.off()
}

#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)
  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)
  }
}
# [1] "Survival.Time"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   3 100.22014 6.314064  86.91920 101.53654
# 2        1    pheno1   6  93.76935 8.235696  93.60032  94.88262
# 3        1    pheno1   8 115.24260 7.756984 115.11279 115.81949
# [1] 1

Past versions of “Plot qtl mapping on 69k-5.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-6.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 2

Past versions of “Plot qtl mapping on 69k-7.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-8.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 3

Past versions of “Plot qtl mapping on 69k-9.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-10.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] "Recovery.Time"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   1 188.47009 6.800872 188.08317 189.42004
# 2        1    pheno1  16  29.50467 7.258734  26.76501  29.78912
# [1] 1

Past versions of “Plot qtl mapping on 69k-11.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-12.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 2

Past versions of “Plot qtl mapping on 69k-13.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-14.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] "Min.depression"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1   9 97.15519 6.161653 96.10171 124.5827
# [1] 1

Past versions of “Plot qtl mapping on 69k-15.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-16.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] "Status_bin"
#   lodindex lodcolumn chr       pos      lod      ci_lo     ci_hi
# 1        1    pheno1   4 156.17629 7.090528 156.009474 156.49607
# 2        1    pheno1   9  68.16325 6.104652  67.850302  68.56932
# 3        1    pheno1  10  29.38717 6.470057   5.600518  68.73517
# 4        1    pheno1  12 108.10231 6.730559  25.430755 109.67503
# 5        1    pheno1  14 120.28595 6.208071 104.068913 121.29650
# 6        1    pheno1  17  27.00602 6.571641  26.634222  85.12396
# 7        1    pheno1  18  85.35144 6.635902  81.255418  86.51269
# 8        1    pheno1   X 144.48572 7.929565 143.604522 145.79861
# [1] 1

Past versions of “Plot qtl mapping on 69k-17.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-18.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 2

Past versions of “Plot qtl mapping on 69k-19.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-20.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 3

Past versions of “Plot qtl mapping on 69k-21.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-22.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 4

Past versions of “Plot qtl mapping on 69k-23.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-24.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 5

Past versions of “Plot qtl mapping on 69k-25.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-26.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 6

Past versions of “Plot qtl mapping on 69k-27.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-28.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 7

Past versions of “Plot qtl mapping on 69k-29.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-30.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 8

Past versions of “Plot qtl mapping on 69k-31.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69k-32.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

#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)
  fname <- paste("output/DO_morphine_secondbatch_",i,"_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)
  }
  dev.off()
}
# [1] "Survival.Time"
# [1] 1
# [1] 2
# [1] 3
# [1] "Recovery.Time"
# [1] 1
# [1] 2
# [1] "Min.depression"
# [1] 1
# [1] "Status_bin"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] 5
# [1] 6
# [1] 7
# [1] 8

#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)
  fname <- paste("output/DO_morphine_secondbatch_",i,"_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)
  }
  dev.off()
}
# [1] "Survival.Time"
# [1] 1
# [1] 2
# [1] 3
# [1] "Recovery.Time"
# [1] 1
# [1] 2
# [1] "Min.depression"
# [1] 1
# [1] "Status_bin"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] 5
# [1] 6
# [1] 7
# [1] 8

Plot qtl mapping on 69K_m2

Plot by using its output qtl.morphine.69k.out.combined_m2.RData

load("output/qtl.morphine.69k.out.combined_m2.RData")
#pmap and gmap
load("data/69k_grid_pgmap.RData")

#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 on 69K_m2-1.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-2.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-3.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-4.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

#save genome-wide plot
for(i in names(qtl.morphine.out)){
  png(file = paste0("output/DO_morphine_combined_69k_m2_", i, ".png"), width = 16, height =8, res=300, units = "in")
  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))
  dev.off()
}

#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)
  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)
  }
}
# [1] "Survival.Time"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1   6 93.76935 6.696094 93.60032 94.88262
# [1] 1

Past versions of “Plot qtl mapping on 69K_m2-5.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-6.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] "Recovery.Time"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1  16 29.08447 6.148843 26.48461 29.65254
# [1] 1

Past versions of “Plot qtl mapping on 69K_m2-7.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-8.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] "Min.depression"
#   lodindex lodcolumn chr       pos      lod    ci_lo     ci_hi
# 1        1    pheno1   6  94.75287 6.074533 93.60032  95.01174
# 2        1    pheno1   9 124.11695 6.070446 96.69146 124.58265
# [1] 1

Past versions of “Plot qtl mapping on 69K_m2-9.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-10.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 2

Past versions of “Plot qtl mapping on 69K_m2-11.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-12.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] "Status_bin"
#   lodindex lodcolumn chr       pos      lod      ci_lo     ci_hi
# 1        1    pheno1   4 156.17629 6.857142 156.009474 156.49607
# 2        1    pheno1   7 115.16657 6.012871 114.526442 115.46115
# 3        1    pheno1  10  29.38717 6.819337   8.597626  33.97126
# 4        1    pheno1  11  37.81053 7.082165  35.662586  38.39621
# 5        1    pheno1  12 107.91869 6.389835 107.816680 109.67503
# 6        1    pheno1  17  27.00602 7.424161  26.634222  28.58929
# 7        1    pheno1  18  85.49980 7.067088  81.327205  86.51269
# 8        1    pheno1   X 144.48572 7.256846 143.604522 145.79861
# [1] 1

Past versions of “Plot qtl mapping on 69K_m2-13.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-14.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 2

Past versions of “Plot qtl mapping on 69K_m2-15.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-16.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 3

Past versions of “Plot qtl mapping on 69K_m2-17.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-18.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 4

Past versions of “Plot qtl mapping on 69K_m2-19.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-20.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 5

Past versions of “Plot qtl mapping on 69K_m2-21.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-22.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 6

Past versions of “Plot qtl mapping on 69K_m2-23.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-24.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 7

Past versions of “Plot qtl mapping on 69K_m2-25.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-26.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

# [1] 8

Past versions of “Plot qtl mapping on 69K_m2-27.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

Past versions of “Plot qtl mapping on 69K_m2-28.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
422da68	xhyuo	2020-07-12

#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)
  fname <- paste("output/DO_morphine_combined_69k_m2_",i,"_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)
  }
  dev.off()
}
# [1] "Survival.Time"
# [1] 1
# [1] "Recovery.Time"
# [1] 1
# [1] "Min.depression"
# [1] 1
# [1] 2
# [1] "Status_bin"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] 5
# [1] 6
# [1] 7
# [1] 8

#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)
  fname <- paste("output/DO_morphine_combined_69k_m2_",i,"_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)
  }
  dev.off()
}
# [1] "Survival.Time"
# [1] 1
# [1] "Recovery.Time"
# [1] 1
# [1] "Min.depression"
# [1] 1
# [1] 2
# [1] "Status_bin"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] 5
# [1] 6
# [1] 7
# [1] 8

Plot qtl mapping on array male

load("output/qtl.morphine.out.combined_gm.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]] <-  combined_gm$gmap[[chr]]
  pmap[[chr]] <-  combined_gm$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_morphine_",i))
}

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

#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)
  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] "Survival.Time"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   2  84.22989 6.046307  75.76507 162.24291
# 2        1    pheno1   3 138.79100 6.380273  64.39701 141.65520
# 3        1    pheno1   4  16.97218 6.542984  16.62465  18.61874
# 4        1    pheno1   6 147.65112 8.516164  93.37250 147.95398
# 5        1    pheno1   8  48.93015 6.406429  45.94523  49.27541
# 6        1    pheno1  10 120.58604 6.749862 119.72620 124.20834
# 7        1    pheno1  11 117.48686 7.807276 117.09262 117.56616
# 8        1    pheno1   X  48.33118 6.518895  42.26096  98.87872
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 3

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 4

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 5

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 6

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 7

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 8

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] "Recovery.Time"
#   lodindex lodcolumn chr       pos      lod    ci_lo     ci_hi
# 1        1    pheno1   1 188.13243 7.053141 187.4489 188.56172
# 2        1    pheno1   2 116.23927 7.091868 114.6279 117.24777
# 3        1    pheno1   7 134.72640 6.233802 134.1477 134.83353
# 4        1    pheno1  19  15.78318 6.236367  11.6891  16.37066
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 3

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 4

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] "Min.depression"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1  15 70.21387 6.737292 67.74024 72.24396
# 2        1    pheno1  18 27.95989 6.788787 27.78975 28.82732
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] "Status_bin"
#   lodindex lodcolumn chr      pos      lod    ci_lo    ci_hi
# 1        1    pheno1  15 87.79636 7.389801 87.42813 88.11448
# 2        1    pheno1   X 41.44546 6.867848 36.58281 42.28244
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

Plot qtl mapping on array female

load("output/qtl.morphine.out.combined_gm.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]] <-  combined_gm$gmap[[chr]]
  pmap[[chr]] <-  combined_gm$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_morphine_",i))
}

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

#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)
  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] "Survival.Time"
#   lodindex lodcolumn chr       pos       lod     ci_lo     ci_hi
# 1        1    pheno1   3  87.75328  7.363908  87.01462  88.24094
# 2        1    pheno1   8 115.47006 10.018661 115.13712 115.57484
# 3        1    pheno1   9  67.05514  7.297535  65.50554  67.16519
# 4        1    pheno1  15  29.63536  7.380134  28.36166  30.77732
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 3

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 4

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] "Recovery.Time"
#   lodindex lodcolumn chr       pos      lod      ci_lo     ci_hi
# 1        1    pheno1   3 118.12137 7.879474 117.724824 121.19240
# 2        1    pheno1   5  92.74391 6.788068  37.152061  97.94610
# 3        1    pheno1   6 110.10532 6.075225 103.818523 140.20546
# 4        1    pheno1  16  28.53624 6.114898  27.599995  29.50554
# 5        1    pheno1  17  11.31727 6.342205   8.947284  12.16295
# 6        1    pheno1  19  31.56747 6.122590  31.188745  61.13260
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 3

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 4

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 5

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 6

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] "Min.depression"
#   lodindex lodcolumn chr       pos      lod      ci_lo     ci_hi
# 1        1    pheno1   4 156.19609 6.005957   9.858468 156.25473
# 2        1    pheno1  10 125.55489 6.017892 125.435827 126.91023
# 3        1    pheno1  19  58.87562 6.340088  42.445420  59.03354
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 3

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] "Status_bin"
#   lodindex lodcolumn chr        pos      lod      ci_lo     ci_hi
# 1        1    pheno1   2  44.052851 6.865421  43.981019  44.45340
# 2        1    pheno1   4 156.164170 7.313472  11.650579 156.22250
# 3        1    pheno1   5  75.711735 6.031017  74.447060 140.84978
# 4        1    pheno1   6 143.410744 8.741595 142.860829 144.10696
# 5        1    pheno1   9  68.163768 8.619578  67.950946  68.33918
# 6        1    pheno1  10   9.053339 6.040880   7.721133 120.73537
# 7        1    pheno1  14 120.707152 7.088220 103.551070 121.45855
# 8        1    pheno1  19  58.715653 6.486409  55.101359  60.04661
# 9        1    pheno1   X 144.599251 8.636026 143.607480 145.35755
# [1] 1

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 3

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 4

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 5

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 6

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 7

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 8

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 9

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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] readxl_1.3.1    abind_1.4-5     regress_1.3-21  survival_3.2-7 
# [5] qtl2_0.24       GGally_2.1.0    gridExtra_2.3   ggplot2_3.3.3  
# [9] workflowr_1.6.2
# 
# loaded via a namespace (and not attached):
#  [1] tidyselect_1.1.0   xfun_0.21          purrr_0.3.4        lattice_0.20-41   
#  [5] splines_4.0.3      colorspace_2.0-0   vctrs_0.3.6        generics_0.1.0    
#  [9] htmltools_0.5.1.1  yaml_2.2.1         blob_1.2.1         rlang_1.0.2       
# [13] later_1.1.0.1      pillar_1.4.7       glue_1.4.2         withr_2.4.1       
# [17] DBI_1.1.1          bit64_4.0.5        RColorBrewer_1.1-2 lifecycle_1.0.0   
# [21] plyr_1.8.6         stringr_1.4.0      cellranger_1.1.0   munsell_0.5.0     
# [25] gtable_0.3.0       evaluate_0.14      memoise_2.0.0      labeling_0.4.2    
# [29] knitr_1.31         fastmap_1.1.0      httpuv_1.5.5       highr_0.8         
# [33] Rcpp_1.0.6         promises_1.2.0.1   scales_1.1.1       cachem_1.0.4      
# [37] farver_2.0.3       fs_1.5.0           bit_4.0.4          digest_0.6.27     
# [41] stringi_1.5.3      dplyr_1.0.4        grid_4.0.3         rprojroot_2.0.2   
# [45] cli_2.3.0          tools_4.0.3        magrittr_2.0.1     tibble_3.0.6      
# [49] RSQLite_2.2.3      crayon_1.4.1       whisker_0.4        pkgconfig_2.0.3   
# [53] Matrix_1.3-2       ellipsis_0.3.1     data.table_1.13.6  assertthat_0.2.1  
# [57] rmarkdown_2.6      reshape_0.8.8      R6_2.5.0           git2r_0.28.0      
# [61] compiler_4.0.3

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