Last updated: 2020-02-25
Checks: 7 0
Knit directory: csna_workflow/
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Unstaged changes:
Modified: README.md
Modified: _workflowr.yml
Modified: analysis/01_geneseek2qtl2.R
Modified: analysis/02_geneseek2intensity.R
Modified: analysis/03_firstgm2genoprobs.R
Modified: analysis/04_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/06_final_pr_apr_69K.R
Modified: analysis/07.1_html_founder_prop.R
Modified: analysis/07_recomb_size_founder_prop.R
Modified: analysis/08_gcta_herit.R
Modified: analysis/09_qtlmapping.R
Modified: analysis/10_qtl_permu.R
Modified: analysis/11_qtl_blup.R
Modified: analysis/run_01_geneseek2qtl2.R
Modified: analysis/run_02_geneseek2intensity.R
Modified: analysis/run_03_firstgm2genoprobs.R
Modified: analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/run_06_final_pr_apr_69K.R
Modified: analysis/run_07.1_html_founder_prop.R
Modified: analysis/run_07_recomb_size_founder_prop.R
Modified: analysis/run_08_gcta_herit.R
Modified: analysis/run_09_qtlmapping.R
Modified: analysis/run_10_qtl_permu.R
Modified: analysis/run_11_qtl_blup.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
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| Rmd | 2fa487b | xhyuo | 2020-02-25 | four_plots_Rmd |
| html | a8606a2 | xhyuo | 2020-02-25 | Build site. |
| Rmd | e5f1857 | xhyuo | 2020-02-25 | 12_plot_qtl_mapping_2.Rmd |
| html | 6861ae7 | xhyuo | 2020-02-16 | Build site. |
| Rmd | 84b8f4a | xhyuo | 2020-02-13 | 12_plot_qtl_mapping_2.Rmd |
| html | c5ca735 | xhyuo | 2020-01-07 | Build site. |
| Rmd | 63566c4 | xhyuo | 2020-01-07 | 12_plot_qtl_mapping_1_2.Rmd |
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| Rmd | 867a8b9 | xhyuo | 2019-10-02 | 12_plot_qtl_mapping_2.Rmd |
| html | e79d270 | xhyuo | 2019-10-02 | Build site. |
| Rmd | 31226ac | xhyuo | 2019-10-02 | 12_plot_qtl_mapping_2.Rmd |
This script will plot the qtl mapping results.
library(qtl2)
library(ggplot2)
load("data/Jackson_Lab_11_batches/gm_DO2816_qc.RData")
pheno <- read.csv("data/pheno/Novelty_residuals_RankNormal_datarelease_12182019.csv", header = TRUE)print("m1")
load("output/m1.Novelty_residuals_RankNormal_datarelease_12182019.RData")
#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
# operm <- list()
# for(i in 3:5){
# operm[[i]] <- get(load(paste0("output/permu/m1_Novelty_residuals_RankNormal_datarelease_12182019_", colnames(pheno)[14], "_", i, ".RData")))
# operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
# }
# operm <- matrix(do.call(rbind, operm[3:5]),ncol = 1)
# class(operm) <- c("scan1perm", "matrix")
# cutoff <- summary(operm, c(0.05, 0.1))[,1]
#genome-wide results
pdf(file = paste0("output/m1.Novelty_residuals_RankNormal_datarelease_12182019", "_genomescan.pdf"), width = 14)
for(i in names(m1.qtl.out)){
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(m1.qtl.out[[i]]) # overall maximum LOD score
plot(m1.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
col="slateblue", ylim=c(0, ymx*1.02),
main=i)
# abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
# abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()
for(i in names(m1.qtl.out)){
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(m1.qtl.out[[i]]) # overall maximum LOD score
plot(m1.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
col="slateblue", ylim=c(0, ymx*1.02),
main=i)
# abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
# abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
y <- get(load(paste0("output/blup/m1_blup_Novelty_residuals_RankNormal_datarelease_12182019_",i,".RData")))
x[[i]] <- y[[i]]
}
m1.blup = x
#coeffects plot
pdf(file = paste0("output/m1.Novelty_residuals_RankNormal_datarelease_12182019", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m1.qtl.out)){
chr <- as.character(m1.peak[[i]][m1.peak[[i]]$lodcolumn == i,"chr"])
par(mar=c(4.1, 4.1, 1.6, 1.6))
plot_coefCC(m1.coef[[i]],
gm_DO2816_qc$gmap[chr],
scan1_output=m1.qtl.out[[i]],
bgcolor="gray95", #legend="bottomleft",
main =i)
plot_coefCC(m1.blup[[i]],
gm_DO2816_qc$gmap[chr],
scan1_output=m1.qtl.out[[i]],
bgcolor="gray95", #legend="bottomleft",
main =i)
# plot(m1.snps[[i]]$lod,
# m1.snps[[i]]$snpinfo,
# drop_hilit=1.5,
# genes=m1.genes[[i]],
# main = i)
}
dev.off()print("m2")[1] "m2"load("output/m2.Novelty_residuals_RankNormal_datarelease_12182019.RData")
#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
operm <- list()
for(i in 1:50){
operm[[i]] <- get(load(paste0("output/permu/m2_Novelty_residuals_RankNormal_datarelease_12182019_", colnames(pheno)[14], "_", i, ".RData")))
operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
}
operm <- matrix(do.call(rbind, operm[1:50]),ncol = 1)
class(operm) <- c("scan1perm", "matrix")
cutoff <- summary(operm, c(0.05, 0.1))[,1]
#genome-wide results
pdf(file = paste0("output/m2.Novelty_residuals_RankNormal_datarelease_12182019", "_genomescan.pdf"), width = 14)
for(i in names(m2.qtl.out)){
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(m2.qtl.out[[i]])*1.2 # overall maximum LOD score
ymax <- ifelse(ymx > cutoff[1]*1.2, ymx, cutoff[1]*1.2)
plot(m2.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
col="slateblue", ylim=c(0, ymax),
main=i)
abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()png
2 #for(i in names(m2.qtl.out)){
# par(mar=c(5.1, 4.1, 1.1, 1.1))
# ymx <- maxlod(m2.qtl.out[[i]]) # overall maximum LOD score
# plot(m2.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
# col="slateblue", ylim=c(0, ymx*1.02),
# main=i)
# abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
# abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
#}
#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
y <- get(load(paste0("output/blup/m2_blup_Novelty_residuals_RankNormal_datarelease_12182019_",i,".RData")))
x[[i]] <- y[[i]]
}
m2.blup = x
#coeffects plot
pdf(file = paste0("output/m2.Novelty_residuals_RankNormal_datarelease_12182019", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m2.qtl.out)){
chr <- as.character(m2.peak[[i]][m2.peak[[i]]$lodcolumn == i,"chr"])
par(mar=c(4.1, 4.1, 1.6, 1.6))
# plot_coefCC(m2.coef[[i]],
# gm_DO2816_qc$gmap[chr],
# scan1_output=m2.qtl.out[[i]],
# bgcolor="gray95", #legend="bottomleft",
# main =i)
plot_coefCC(m2.blup[[i]],
gm_DO2816_qc$gmap[chr],
scan1_output=m2.qtl.out[[i]],
bgcolor="gray95", #legend="bottomleft",
main =i)
# plot(m2.snps[[i]]$lod,
# m2.snps[[i]]$snpinfo,
# drop_hilit=1.5,
# genes=m2.genes[[i]],
# main = i)
}
dev.off()png
2 for(i in names(m2.qtl.out)){
print(i)
if(is.null(m2.snps[[i]]))
next
top_1 <- data.frame(pheno = i)
top <- top_snps(m2.snps[[i]]$lod, m2.snps[[i]]$snpinfo)
top <- cbind(top_1, top)
write.table(top, file = "output/Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", sep = ",",
row.names = F, col.names = T, append = TRUE)
topgene <- cbind(top_1, m2.genes[[i]])
write.table(topgene, file = "output/Novelty_residuals_RankNormal_datarelease_12182019-genelist.csv", sep = ",",
row.names = F, col.names = T, append = TRUE)
}[1] "OFA.total.distance.traveled"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to fileWarning in write.table(topgene, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-genelist.csv", :
appending column names to file[1] "OFA.distance.traveled.slope"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.time.in.corner"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.time.in.perimeter"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.time.in.center"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.ambulatory.time"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.distance.traveled.in.perimeter"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.distance.traveled.in.center"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.total.distance.traveled.in.corner"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.pct.dist.center"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.pct.dist.corner"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.pct.dist.perimeter"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.pct.time.center"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.pct.time.corner"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.pct.time.perimeter"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.distance.traveled.first.five"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "OFA.distance.traveled.last.five"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "LD.pct.distance.traveled.in.light"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "LD.pct.ambulatory.time.in.light"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "LD.pct.resting.time.in.light"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "LD.pct.time.in.light"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "LD.pct.ambulatory.Counts.in.light"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "LD.total.transitions"
[1] "HB.Total.Entries"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "HB.Novel.Entries"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "HB.Repeat.Entries"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "NPP.NoveltyPreference.ZoneTime_WhiteVsBlack_Total"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file[1] "NPP.NoveltyPreference.ZoneTime_GreyWhiteBlack_Total"Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to file
Warning in write.table(top, file = "output/
Novelty_residuals_RankNormal_datarelease_12182019-variantlist.csv", :
appending column names to fileprint("m3")
load("output/m3.Novelty_residuals_RankNormal_datarelease_12182019.RData")
#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
# operm <- list()
# for(i in 3:5){
# operm[[i]] <- get(load(paste0("output/permu/m3_Novelty_residuals_RankNormal_datarelease_12182019_", colnames(pheno)[14], "_", i, ".RData")))
# operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
# }
# operm <- matrix(do.call(rbind, operm[3:5]),ncol = 1)
# class(operm) <- c("scan1perm", "matrix")
# cutoff <- summary(operm, c(0.05, 0.1))[,1]
#genome-wide results
pdf(file = paste0("output/m3.Novelty_residuals_RankNormal_datarelease_12182019", "_genomescan.pdf"), width = 14)
for(i in names(m3.qtl.out)){
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(m3.qtl.out[[i]]) # overall maximum LOD score
plot(m3.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
col="slateblue", ylim=c(0, ymx*1.02),
main=i)
# abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
# abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()
for(i in names(m3.qtl.out)){
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(m3.qtl.out[[i]]) # overall maximum LOD score
plot(m3.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
col="slateblue", ylim=c(0, ymx*1.02),
main=i)
# abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
# abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
y <- get(load(paste0("output/blup/m3_blup_Novelty_residuals_RankNormal_datarelease_12182019_",i,".RData")))
x[[i]] <- y[[i]]
}
m3.blup = x
#coeffects plot
pdf(file = paste0("output/m3.Novelty_residuals_RankNormal_datarelease_12182019", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m3.qtl.out)){
chr <- as.character(m3.peak[[i]][m3.peak[[i]]$lodcolumn == i,"chr"])
par(mar=c(4.1, 4.1, 1.6, 1.6))
plot_coefCC(m3.coef[[i]],
gm_DO2816_qc$gmap[chr],
scan1_output=m3.qtl.out[[i]],
bgcolor="gray95", #legend="bottomleft",
main =i)
plot_coefCC(m3.blup[[i]],
gm_DO2816_qc$gmap[chr],
scan1_output=m3.qtl.out[[i]],
bgcolor="gray95", #legend="bottomleft",
main =i)
# plot(m3.snps[[i]]$lod,
# m3.snps[[i]]$snpinfo,
# drop_hilit=1.5,
# genes=m3.genes[[i]],
# main = i)
}
dev.off()
sessionInfo()R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.1.0 qtl2_0.18
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 pillar_1.3.1 git2r_0.23.0
[4] plyr_1.8.4 workflowr_1.4.0 tools_3.3.2
[7] digest_0.6.18 bit_1.1-14 RSQLite_2.1.1
[10] evaluate_0.10 memoise_1.1.0 tibble_2.1.3
[13] gtable_0.2.0 pkgconfig_2.0.1 rlang_0.4.0
[16] DBI_1.0.0 yaml_2.2.0 parallel_3.3.2
[19] withr_2.1.2 stringr_1.3.1 dplyr_0.8.3
[22] knitr_1.20 fs_1.2.6 rprojroot_1.3-2
[25] bit64_0.9-7 grid_3.3.2 tidyselect_0.2.5
[28] glue_1.3.1 data.table_1.11.4 R6_2.4.0
[31] rmarkdown_1.11 purrr_0.3.2 blob_1.1.1
[34] magrittr_1.5 whisker_0.3-2 backports_1.1.2
[37] scales_1.0.0 htmltools_0.3.6 assertthat_0.2.1
[40] colorspace_1.4-0 stringi_1.2.4 lazyeval_0.2.1
[43] munsell_0.5.0 crayon_1.3.4