## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, fig.width = 7, fig.height = 5) ## ----------------------------------------------------------------------------- library(qtl2ggplot) library(ggplot2) ## ----------------------------------------------------------------------------- DOex <- qtl2::read_cross2( file.path( "https://raw.githubusercontent.com/rqtl", "qtl2data/master/DOex", "DOex.zip")) ## ----------------------------------------------------------------------------- tmpfile <- tempfile() file <- paste0("https://raw.githubusercontent.com/rqtl/", "qtl2data/master/DOex/DOex_alleleprobs.rds") download.file(file, tmpfile) apr <- readRDS(tmpfile) unlink(tmpfile) ## ----eval = FALSE------------------------------------------------------------- # pr <- qtl2::calc_genoprob(DOex, error_prob=0.002) # apr <- qtl2::genoprob_to_alleleprob(pr) ## ----------------------------------------------------------------------------- scan_apr <- qtl2::scan1(apr, DOex$pheno) ## ----------------------------------------------------------------------------- qtl2::find_peaks(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- summary(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- plot(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- autoplot(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- DOex <- DOex[,"2"] apr <- subset(apr, chr = "2") ## ----------------------------------------------------------------------------- scan_apr <- qtl2::scan1(apr, DOex$pheno) ## ----------------------------------------------------------------------------- qtl2::find_peaks(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- plot(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- autoplot(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- coefs <- qtl2::scan1coef(apr, DOex$pheno) ## ----------------------------------------------------------------------------- summary(coefs, scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- plot(coefs, DOex$pmap, 1:8, col = qtl2::CCcolors) ## ----------------------------------------------------------------------------- autoplot(coefs, DOex$pmap) ## ----------------------------------------------------------------------------- plot(coefs, DOex$pmap, 1:8, col = qtl2::CCcolors, scan1_output = scan_apr) ## ----------------------------------------------------------------------------- autoplot(coefs, DOex$pmap, scan1_output = scan_apr, legend.position = "none") ## ----------------------------------------------------------------------------- plot(coefs, DOex$pmap, c(5,8), col = qtl2::CCcolors[c(5,8)]) ## ----------------------------------------------------------------------------- autoplot(coefs, DOex$pmap, c(5,8)) ## ----------------------------------------------------------------------------- autoplot(coefs, DOex$pmap, c(5,8), facet = "geno") ## ----------------------------------------------------------------------------- plot(coefs, DOex$pmap, 4:5, col = qtl2::CCcolors[4:5], scan1_output = scan_apr) ## ----------------------------------------------------------------------------- autoplot(coefs, DOex$pmap, 4:5, scan1_output = scan_apr, legend.position = "none") ## ----------------------------------------------------------------------------- tmpfile <- tempfile() file <- paste0("https://raw.githubusercontent.com/rqtl/", "qtl2data/master/DOex/DOex_genoprobs.rds") download.file(file, tmpfile) pr <- readRDS(tmpfile) unlink(tmpfile) pr <- subset(pr, chr = "2") ## ----eval = FALSE------------------------------------------------------------- # pr <- qtl2::calc_genoprob(DOex, error_prob=0.002) ## ----------------------------------------------------------------------------- filename <- file.path("https://raw.githubusercontent.com/rqtl", "qtl2data/master/DOex", "c2_snpinfo.rds") tmpfile <- tempfile() download.file(filename, tmpfile, quiet=TRUE) snpinfo <- readRDS(tmpfile) unlink(tmpfile) ## ----eval = FALSE------------------------------------------------------------- # snpdb_file <- system.file("extdata", "cc_variants_small.sqlite", package="qtl2") # query_variant <- qtl2::create_variant_query_func(snpdb_file) # snpinfo <- query_variant("2", 96.5, 98.5) ## ----------------------------------------------------------------------------- variants <- c("snp","indel","SV","INS","DEL","INV") snpinfo$type <- factor( sample( c(sample(variants[-1], 5000, replace = TRUE), rep("snp", nrow(snpinfo) - 5000))), variants) ## ----------------------------------------------------------------------------- snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo) snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo) scan_snppr <- qtl2::scan1(snppr, DOex$pheno) ## ----------------------------------------------------------------------------- plot(scan_snppr, snpinfo, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- plot(scan_snppr, snpinfo, show_all_snps=FALSE, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, show_all_snps=FALSE, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- plot(scan_snppr, snpinfo, drop_hilit=1.5, cex=1, pch=1) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, drop_hilit=1.5, cex=2) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, patterns="all", drop_hilit=3, cex=2) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, patterns="hilit", drop_hilit=3, cex=2) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, patterns="hilit", drop_hilit=3, cex=2, show_all_snps = FALSE) ## ----------------------------------------------------------------------------- filename <- file.path("https://raw.githubusercontent.com/rqtl", "qtl2data/master/DOex", "c2_genes.rds") tmpfile <- tempfile() download.file(filename, tmpfile, quiet=TRUE) gene_tbl <- readRDS(tmpfile) unlink(tmpfile) ## ----eval=FALSE--------------------------------------------------------------- # dbfile <- system.file("extdata", "mouse_genes_small.sqlite", package="qtl2") # query_genes <- qtl2::create_gene_query_func(dbfile, filter="(source=='MGI')") # gene_tbl <- query_genes("2", 96.5, 98.5) ## ----------------------------------------------------------------------------- qtl2::plot_genes(gene_tbl, xlim = c(96,99)) ## ----------------------------------------------------------------------------- ggplot_genes(gene_tbl) ## ----------------------------------------------------------------------------- DOex$pheno <- cbind(DOex$pheno, asin = asin(sqrt(DOex$pheno[,1] / 100))) ## ----------------------------------------------------------------------------- scan_apr <- qtl2::scan1(apr, DOex$pheno) ## ----------------------------------------------------------------------------- qtl2::find_peaks(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- summary(scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- plot(scan_apr, DOex$pmap, 1) plot(scan_apr, DOex$pmap, 2, add = TRUE, col = "red") ## ----------------------------------------------------------------------------- autoplot(scan_apr, DOex$pmap, 1:2) ## ----------------------------------------------------------------------------- autoplot(scan_apr, DOex$pmap, 1:2, facet="pheno", scales = "free_x", shape = "free_x") ## ----------------------------------------------------------------------------- scan_snppr <- qtl2::scan1(snppr, DOex$pheno) ## ----------------------------------------------------------------------------- summary(scan_snppr, DOex$pmap, snpinfo) ## ----------------------------------------------------------------------------- plot(scan_snppr, snpinfo, lodcolumn=1, cex=1, pch=1, drop_hilit = 1.5) plot(scan_snppr, snpinfo, lodcolumn=2, cex=1, pch=1, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 1:2, facet="pheno", drop_hilit = 1.5) ## ----------------------------------------------------------------------------- plot(scan_snppr, snpinfo, lodcolumn=1, cex=1, pch=1, show_all_snps = FALSE, drop_hilit = 1.5) plot(scan_snppr, snpinfo, lodcolumn=2, cex=1, pch=1, show_all_snps = FALSE, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 1:2, show_all_snps = FALSE, facet="pheno", cex=2, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 2, show_all_snps = FALSE, facet="pheno", cex=2, drop_hilit = 1.5) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 1:2,show_all_snps = FALSE, facet_var = "pheno", drop_hilit = 2, col=8, col_hilit=1:2, cex=2) + geom_hline(yintercept = max(scan_snppr) - 2, col = "darkgrey", linetype = "dashed") ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 2, patterns = "all", cex=2, drop_hilit=2) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 1:2, patterns = "all", cex=2, facet = "pheno", drop_hilit=3) ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 1:2, patterns = "hilit", cex=2, drop_hilit=3, facet = "pheno", scales = "free") ## ----------------------------------------------------------------------------- autoplot(scan_snppr, snpinfo, 1:2, patterns = "hilit", show_all_snps = TRUE, cex=2, drop_hilit=3, facet = "pattern") ## ----------------------------------------------------------------------------- (peaks <- qtl2::find_peaks(scan_apr, DOex$pmap, drop = 1.5)) ## ----------------------------------------------------------------------------- qtl2::plot_peaks(peaks, DOex$pmap) ## ----------------------------------------------------------------------------- ggplot_peaks(peaks, DOex$pmap) ## ----------------------------------------------------------------------------- out <- listof_scan1coef(apr, DOex$pheno, center = TRUE) ## ----------------------------------------------------------------------------- summary(out, scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- ggplot2::autoplot(out, DOex$pmap, scales = "free") ## ----------------------------------------------------------------------------- summary(out, scan_apr, DOex$pmap) ## ----------------------------------------------------------------------------- coefs36 <- qtl2::scan1coef(pr, DOex$pheno) ## ----------------------------------------------------------------------------- plot(coefs36, DOex$pmap, 1:36, col = 1:36, ylim=c(-100,100)) ## ----------------------------------------------------------------------------- autoplot(coefs36, DOex$pmap, ylim=c(-100,100), colors = NULL, legend.position = "none") ## ----------------------------------------------------------------------------- autoplot(coefs36, DOex$pmap, ylim=c(-100,100), center = FALSE, colors = NULL, legend.position = "none") ## ----------------------------------------------------------------------------- tmp <- qtl2ggplot:::modify_object(coefs36, coefs36[, stringr::str_detect(dimnames(coefs36)[[2]], "E")]) autoplot(tmp, DOex$pmap, ylim=c(-100,100))