Plot_DO_morphine

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Last updated: 2023-02-21

Checks: 7 0

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.Rmd) and HTML (docs/Plot_DO_morphine.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.
html	c9ed9ff	xhyuo	2020-05-29	Build site.
Rmd	3277c6d	xhyuo	2020-05-29	Plot_DO_morphine at helix

---

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)

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

do.pheno <- read.csv("data/pheno_qtl2.csv")
do.pheno$Survival.Time <- as.numeric(do.pheno$Survival.Time)
do.pheno$Recovery.Time <- as.numeric(do.pheno$Recovery.Time)
do.pheno$Min.depression <- as.numeric(do.pheno$Min.depression)

#histogram
a <- ggplot(data=do.pheno, aes(do.pheno$Survival.Time)) + 
  geom_histogram() +
  ylab("Number of DO mice") + xlab("Survival Time (h)")
  
b <- ggplot(data=do.pheno, aes(do.pheno$Recovery.Time)) + 
  geom_histogram() +
  ylab("Number of DO mice") + xlab("Recovery Time (h)")

c <- ggplot(data=do.pheno, aes(do.pheno$Min.depression)) + 
  geom_histogram() +
  ylab("Number of DO mice") + xlab("Respiratory Depression (% of baseline)")

grid.arrange(a,b,c)
# Warning: Use of `do.pheno$Survival.Time` is discouraged. Use `Survival.Time`
# instead.
# Warning: Removed 198 rows containing non-finite values (stat_bin).
# Warning: Use of `do.pheno$Recovery.Time` is discouraged. Use `Recovery.Time`
# instead.
# Warning: Removed 121 rows containing non-finite values (stat_bin).
# Warning: Use of `do.pheno$Min.depression` is discouraged. Use `Min.depression`
# instead.
# Warning: Removed 27 rows containing non-finite values (stat_bin).

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

d <- ggpairs(do.pheno[,2:4])
d
# Warning: Removed 198 rows containing non-finite values (stat_density).
# Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
# Removed 215 rows containing missing values
# Warning: Removed 121 rows containing non-finite values (stat_density).
# Warning in ggally_statistic(data = data, mapping = mapping, na.rm = na.rm, :
# Removed 124 rows containing missing values
# Warning: Removed 215 rows containing missing values (geom_point).
# Warning: Removed 124 rows containing missing values (geom_point).
# Warning: Removed 27 rows containing non-finite values (stat_density).

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

Plot qtl mapping

DO_morphine1.sh/DO_morphine1.R performs qtl mapping for DO mice in DO Opioid project. Plot by using its output qtl.morphine.out.RData

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

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

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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

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c9ed9ff	xhyuo	2020-05-29

#save genome-wide plot
for(i in names(qtl.morphine.out)){
  png(file = paste0("output/DO_morphine_", 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)
  for(p in 1:dim(peaks)[1]) {
    print(p)
    chr <-peaks[p,3]
    #coeff plot
    par(mar=c(4.1, 4.1, 0.6, 0.6))
    plot_coefCC(coef_c1[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
    plot_coefCC(coef_c2[[i]][[p]], pmap[chr], scan1_output=qtl.morphine.out[[i]], bgcolor="gray95", legend="topright")
  }
}
# [1] "Survival.Time"
# [1] 1

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Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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# [1] 2

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

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8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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

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

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8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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c9ed9ff	xhyuo	2020-05-29

# [1] 2

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

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8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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

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

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8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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# [1] 2

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

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c9ed9ff	xhyuo	2020-05-29

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

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

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# [1] 2

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# [1] 3

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# [1] 4

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# [1] 5

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# [1] 6

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# [1] 7

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

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8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

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

#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_",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="topright")
  }
  dev.off()
}
# [1] "Survival.Time"
# [1] 1
# [1] 2
# [1] "Recovery.Time"
# [1] 1
# [1] 2
# [1] "Min.depression"
# [1] 1
# [1] 2
# [1] "Status_bin"
# [1] 1
# [1] 2
# [1] 3
# [1] 4
# [1] 5
# [1] 6
# [1] 7

#SNP association of chr5 for Min.depression
i   = "Min.depression"
par(mar=c(4.1, 4.1, 0.6, 0.6))
plot(out_snps[[i]][[1]]$lod, out_snps[[i]][[1]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[1]])

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

png(file = paste0("output/DO_morphine_", i, "_peak_genes_chr5.png"), width = 16, height =8, res=300, units = "in")
par(mar=c(4.1, 4.1, 0.6, 0.6))
plot(out_snps[[i]][[1]]$lod, out_snps[[i]][[1]]$snpinfo, drop_hilit=1.5, genes=out_genes[[i]][[1]])
dev.off()
# png 
#   2
#SNP table
top <- top_snps(out_snps[[i]][[1]]$lod, out_snps[[i]][[1]]$snpinfo,show_all_snps = T, drop = 1.5)
dim(top)
# [1] 406  20
write.csv(top, file = "output/topSNP_chr5_mindepression.csv", row.names = F)

#violin at chr5 for Min.depression
#need the apr
aprobs <- readRDS(file =  "output/do.morphine.probs_8state.rds")
#morphine pheno
morphine.pheno <- read.csv("data/pheno_qtl2_07092018_morphine.csv",header = T)
rownames(morphine.pheno) <- gsub("morphine_DO_jbubier_","", morphine.pheno$X)

chr = 5
peaks <- find_peaks(qtl.morphine.out[[i]], map=pmap, threshold=6, drop=1.5)
marker <- find_marker(pmap, chr, pos=peaks[peaks$chr==chr, "pos"])
peak_Mbp <- pmap[[chr]][marker]
g <- maxmarg(aprobs, do.morphine$gmap, chr=chr, minprob=0.4, pos=peaks[peaks$chr==chr, "pos"], return_char = TRUE)
stopifnot(all.equal(names(g), rownames(morphine.pheno)))
px <- cbind(g, morphine.pheno)
colnames(px)[1] <- "Strain"
px <- px[!is.na(px$Strain),]
png(paste("output/DO_morphine_Min.depression_violin_chr",chr,".png",sep=""),
    width = 24, height =16, res=300, units = "in")
p <- ggplot(px, aes_string(x="Strain", y="Min.depression", group="Strain", fill="Strain")) +
  geom_violin() +
  geom_point() +
  scale_fill_manual(labels = c("A/J", "C57BL/6J", "129S1/SvImJ", "NOD/ShiLtJ", "NZO/HlLtJ", "CAST/EiJ", "PWK/PhJ", "WSB/EiJ"),
                    values=as.vector(qtl2::CCcolors)) +
  scale_x_discrete(labels=c("A" = "A/J", 
                            "B" = "C57BL/6J",
                            "C" = "129S1/SvImJ", 
                            "D" = "NOD/ShiLtJ",
                            "E" = "NZO/HlLtJ", 
                            "F" = "CAST/EiJ",
                            "G" = "PWK/PhJ",
                            "H" = "WSB/EiJ")) +
  xlab(paste0("marker:", marker, " chr", chr, ":", peak_Mbp, "Mbp")) +
  theme(axis.text.x = element_text(angle = -45, hjust = 0.1, vjust = 0.1),
        text = element_text(size=14))
print(p)
dev.off()
# png 
#   2
p

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

Plot CoxPH results

#markers
pmap_all <- read.csv("data/physical_map.csv", header = T,stringsAsFactors = F)
gmap_all <- read.csv("data/genetic_map.csv", header = T,stringsAsFactors = F)
markers <- data.frame(stringsAsFactors = F,
                      marker = as.character(pmap_all$marker),
                      chr = as.character(pmap_all$chr),
                      pos = as.numeric(pmap_all$pos)*10^6,
                      cM = as.numeric(gmap_all$pos))

rownames(markers) <- markers$marker
markers <- markers[marker_names(do.morphine),]

load("output/DO_morphine_cphout.RData")
out.cph2 <-  as.matrix(out.cph[,1,drop=F])
attr(out.cph2, "class") <- c("scan1", "matrix")
#plot
plot(out.cph2, map = pmap, type = "l", lwd = 1, main = "Do_morphine: COX PH model")

Past versions of “Plot CoxPH results-1.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

#save CoxPH plot
png("output/DO_morphine_coxph_24hrs_kinship_QTL.png", width = 1000, height = 800, res = 128)
plot(out.cph2, map = pmap, type = "l", lwd = 1, main = "Do_morphine: COX PH model")
dev.off()
# png 
#   2

#coeff plot
coef <- out.cph[,c(-1:-9)]
lod <- out.cph[,1]
col = do.colors
col[1,3] = "#FFC000"
for(i in c(1:19, "X")) {
  png(paste0("output/coxph/DO_morphine_coxph_24hrs_kinship_QTL_chr", i, ".png"), width = 1200,
      height = 1000, res = 128)
  rng = which(markers[,2] == i)
  tmp = coef[rng,c(2:ncol(coef))]
  tmp[,1] = 0
  tmp = tmp - rowMeans(tmp)
  colnames(tmp)[1] = "A"

  layout(matrix(1:2, 2, 1), heights = c(0.8, 0.2))
  par(plt = c(0.15, 0.99, 0, 0.9))
  plot(markers[rng,3] * 1e-6, tmp[,1], lwd = 2, type = "l", col = col[1,3],
       main = paste("Do_morphine_coxph_24hrs: COX PH model: Chr", i),
       ylim = range(tmp), las = 1, xaxt = "n", ylab = "")
  mtext(side = 2, line = 4, text = "Founder Effects")
  for(j in 2:8) {
    points(markers[rng,3] * 1e-6, tmp[,j], lwd = 2, type = "l", col = col[j,3])
  } # for(j)

  par(plt = c(0.15, 0.99, 0.25, 1))
  plot(markers[rng,3] * 1e-6, lod[rng], type = "l", las = 1, ylab = "LOD")
  dev.off()

} # for(i)

#remove some noisy markers in chr 2
i = 2
png(paste0("output/coxph/DO_morphine_coxph_24hrs_kinship_QTL_chr", i, ".removesome_markers.png"), width = 1200,height = 1000, res = 128)
rng = which(markers[,2] == i)
tmp = coef[rng,c(2:ncol(coef))]
tmp[,1] = 0
#remove some markers
tmp = tmp[!rownames(tmp) %in% names(which(abs(rowMeans(tmp)) >5000)),]
markers2 = markers[markers$marker %in% rownames(tmp),]
coef2 <- coef[markers2$marker,]
#redo
rng = which(markers2[,2] == i)
tmp = coef[rng,c(2:ncol(coef2))]
tmp[,1] = 0
tmp = tmp - rowMeans(tmp)
colnames(tmp)[1] = "A"

lod2 <- lod[markers2$marker]
print(all.equal(names(lod2),markers2$marker))
# [1] TRUE

layout(matrix(1:2, 2, 1), heights = c(0.8, 0.2))
par(plt = c(0.15, 0.99, 0, 0.9))
plot(markers2[rng,3] * 1e-6, tmp[,1], lwd = 2, type = "l", col = col[1,3],
     main = paste("Do_morphine_coxph_24hrs: COX PH model: Chr", i),
     ylim = range(tmp), las = 1, xaxt = "n", ylab = "")
mtext(side = 2, line = 4, text = "Founder Effects")
for(j in 2:8) {
  points(markers2[rng,3] * 1e-6, tmp[,j], lwd = 2, type = "l", col = col[j,3])
  } # for(j)

par(plt = c(0.15, 0.99, 0.25, 1))
plot(markers2[rng,3] * 1e-6, lod2[rng], type = "l", las = 1, ylab = "LOD")
dev.off()
# png 
#   2
#plot
layout(matrix(1:2, 2, 1), heights = c(0.8, 0.2))
par(plt = c(0.15, 0.99, 0, 0.9))
plot(markers2[rng,3] * 1e-6, tmp[,1], lwd = 2, type = "l", col = col[1,3],
     main = paste("Do_morphine_coxph_24hrs: COX PH model: Chr", i),
     ylim = range(tmp), las = 1, xaxt = "n", ylab = "")
mtext(side = 2, line = 4, text = "Founder Effects")
for(j in 2:8) {
  points(markers2[rng,3] * 1e-6, tmp[,j], lwd = 2, type = "l", col = col[j,3])
  } # for(j)

par(plt = c(0.15, 0.99, 0.25, 1))
plot(markers2[rng,3] * 1e-6, lod2[rng], type = "l", las = 1, ylab = "LOD")

Past versions of “Plot CoxPH results-2.png”

Version	Author	Date
8fe8543	xhyuo	2023-02-20
c9ed9ff	xhyuo	2020-05-29

Plot qtl mapping on array male

load("output/qtl.morphine.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]] <-  do.morphine$gmap[[chr]]
  pmap[[chr]] <-  do.morphine$pmap[[chr]]
}
attr(gmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)
attr(pmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)

#genome-wide plot
for(i in names(qtl.morphine.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(qtl.morphine.out[[i]]) # overall maximum LOD score
  plot(qtl.morphine.out[[i]], map=pmap, lodcolumn=1, col="slateblue", ylim=c(0, 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   2 181.834074 6.319026 20.490494 181.99828
# 2         1    pheno1   3 108.967671 6.539246 25.209613 138.81008
# 3         1    pheno1   4  68.634564 7.419725 64.445383  71.27997
# 4         1    pheno1   6 147.651116 6.788338  4.328042 148.66752
# 5         1    pheno1   7  63.138787 6.862268 13.038070  63.27048
# 6         1    pheno1   8  21.736266 8.977322 19.654408  22.11891
# 7         1    pheno1   9  55.045695 6.795889 54.991021  56.84955
# 8         1    pheno1  11 117.517563 6.488320 63.237669 117.55926
# 9         1    pheno1  12 105.574622 7.253200 74.893565 106.31609
# 10        1    pheno1  14  99.236933 7.843284 47.332527 105.66663
# 11        1    pheno1  17   4.362966 7.240142  3.192903  65.62523
# [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] 9

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] 10

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] 11

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] "Recovery.Time"
#   lodindex lodcolumn chr     pos      lod    ci_lo    ci_hi
# 1        1    pheno1   2 116.336 6.044203 57.38935 117.2478
# [1] 1

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   5 26.203835 6.228551 24.841651 50.24141
# 2        1    pheno1   6 21.240236 6.168790 20.676183 23.20589
# 3        1    pheno1  17  3.257454 6.099197  3.075928 71.51265
# [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] 3

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] "Status_bin"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   1 194.90004 7.231262 194.63822 195.36002
# 2        1    pheno1   8  78.08382 6.071287  78.03203  89.74609
# [1] 1

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

# [1] 2

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

Plot qtl mapping on array female

load("output/qtl.morphine.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]] <-  do.morphine$gmap[[chr]]
  pmap[[chr]] <-  do.morphine$pmap[[chr]]
}
attr(gmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)
attr(pmap, "is_x_chr") <- structure(c(rep(FALSE,19),TRUE), names=1:20)

#genome-wide plot
for(i in names(qtl.morphine.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(qtl.morphine.out[[i]]) # overall maximum LOD score
  plot(qtl.morphine.out[[i]], map=pmap, lodcolumn=1, col="slateblue", ylim=c(0, 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   2 108.20689 6.854241 107.24263 150.00078
# 2        1    pheno1   3  38.52197 6.419152  38.25791 109.66640
# 3        1    pheno1   5 104.19473 8.252319 103.82013 105.66710
# 4        1    pheno1   8 115.25017 6.352567 114.99883 115.26932
# 5        1    pheno1  11  75.15149 6.353510  37.05275  76.42170
# 6        1    pheno1  17  83.99650 6.544571  83.63927  84.29922
# [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] 5

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] 6

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] "Recovery.Time"
#   lodindex lodcolumn chr       pos      lod     ci_lo     ci_hi
# 1        1    pheno1   2  11.42175 7.039471  10.46705  11.90852
# 2        1    pheno1   4  32.07822 6.418205  31.92851  32.86047
# 3        1    pheno1   9 123.06013 6.303715 119.26361 123.62391
# [1] 1

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] 2

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] 3

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] "Min.depression"
#   lodindex lodcolumn chr      pos      lod   ci_lo   ci_hi
# 1        1    pheno1   5 25.05437 6.281007 24.9198 25.6421
# [1] 1

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] "Status_bin"
#    lodindex lodcolumn chr        pos       lod      ci_lo     ci_hi
# 1         1    pheno1   1  19.164865  6.147268  15.439741 192.89712
# 2         1    pheno1   2 105.663925 10.873472 105.124103 106.49603
# 3         1    pheno1   3 138.083675  9.260545 109.677215 141.68062
# 4         1    pheno1   4 155.860646  8.348013 154.284934 156.25473
# 5         1    pheno1   5 100.655515  6.928981  99.534811 134.77861
# 6         1    pheno1   6   5.891843  7.528947   5.832646  13.19729
# 7         1    pheno1   7  69.702691  9.538679  69.411383  69.70587
# 8         1    pheno1   8 121.211859  7.057530  21.823677 121.48475
# 9         1    pheno1   9  18.763008  6.291868  17.554432 111.43643
# 10        1    pheno1  10  24.631651  7.226505  21.331286  26.28567
# 11        1    pheno1  15  93.991656  7.433259  93.880481  94.14353
# 12        1    pheno1  16  89.871019  7.692891  88.692381  90.42208
# 13        1    pheno1  17  69.904861  6.080928  26.641041  70.50038
# 14        1    pheno1  18  73.967036  6.055066  36.069954  74.54257
# 15        1    pheno1  19  58.739120  6.488041  58.674418  59.16199
# [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] 4

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] 5

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] 6

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] 7

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] 8

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] 9

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] 10

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] 11

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] 12

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

# [1] 13

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 14

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

# [1] 15

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

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

Version	Author	Date
8fe8543	xhyuo	2023-02-20

Past versions of “Plot qtl mapping on array female-79.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] abind_1.4-5     regress_1.3-21  survival_3.2-7  qtl2_0.24      
# [5] GGally_2.1.0    gridExtra_2.3   ggplot2_3.3.3   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      munsell_0.5.0      gtable_0.3.0      
# [25] evaluate_0.14      memoise_2.0.0      labeling_0.4.2     knitr_1.31        
# [29] fastmap_1.1.0      httpuv_1.5.5       highr_0.8          Rcpp_1.0.6        
# [33] promises_1.2.0.1   scales_1.1.1       cachem_1.0.4       farver_2.0.3      
# [37] fs_1.5.0           bit_4.0.4          digest_0.6.27      stringi_1.5.3     
# [41] dplyr_1.0.4        grid_4.0.3         rprojroot_2.0.2    cli_2.3.0         
# [45] tools_4.0.3        magrittr_2.0.1     tibble_3.0.6       RSQLite_2.2.3     
# [49] crayon_1.4.1       whisker_0.4        pkgconfig_2.0.3    Matrix_1.3-2      
# [53] ellipsis_0.3.1     data.table_1.13.6  assertthat_0.2.1   rmarkdown_2.6     
# [57] reshape_0.8.8      R6_2.5.0           git2r_0.28.0       compiler_4.0.3

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