# Plot scan pattern usign ggplot2 Plot scan pattern usign ggplot2 Genome scan by pattern set ```r ggplot_scan1pattern( object, map, plot_type = c("lod", "coef", "coef_and_lod"), patterns = object$patterns$founders, columns = 1:3, min_lod = 3, lodcolumn = seq_along(patterns), facet = "pheno", ... ) ## S3 method for class 'scan1pattern' autoplot(object, ...) scan1pattern( probs1, phe, K = NULL, covar = NULL, map, patterns, condense_patterns = TRUE, blups = FALSE, do_scans = TRUE ) ## S3 method for class 'scan1pattern' summary(object, map, ...) ``` ## Arguments - `object`: object of class `scan1pattern` - `map`: genome map - `plot_type`: type of plot from `c("lod","coef")` - `patterns`: data frame of pattern information - `columns`: columns used for coef plot - `min_lod`: minimum LOD peak for contrast to be retained - `lodcolumn`: columns used for scan1 plot (default all `patterns`) - `facet`: Plot facets if multiple phenotypes and patterns provided (default = `"pheno"`). - `...`: additional parameters passed on to other methods - `probs1`: object of class `calc_genoprob` - `phe`: data frame with one phenotype - `K`: kinship matrix - `covar`: covariate matrix - `condense_patterns`: remove snp_action from contrasts if TRUE - `blups`: Create BLUPs if `TRUE` - `do_scans`: Do scans if `TRUE`. ## Returns object of class `ggplot` List containing: * patterns Data frame of summary for top patterns (column `founders` has pattern) * dip_set Diplotype sets for contrasts * group Group for each founder pattern * scan Object of class `scan1`. * coef Object of class `listof_scan1coef`. See package 'qtl2ggplot'. ## Examples ```r dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex" # Read DOex example cross from 'qtl2data' DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2") # Download genotype probabilities tmpfile <- tempfile() download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE) pr <- readRDS(tmpfile) unlink(tmpfile) # Download SNP info for DOex from web and read as RDS. tmpfile <- tempfile() download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE) snpinfo <- readRDS(tmpfile) unlink(tmpfile) snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp) # Convert to SNP probabilities snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo) snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo) # Scan SNPs scan_snppr <- qtl2::scan1(snppr, DOex$pheno) top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo) # Summarize to find top patterns patterns <- dplyr::arrange(summary(top_snps_tbl), dplyr::desc(max_lod)) # Scan using patterns. scan_pat <- scan1pattern(pr, DOex$pheno, map = DOex$pmap, patterns = patterns) # Summary of scan1pattern. summary(scan_pat, DOex$pmap) ``` ## Author(s) Brian S Yandell, brian.yandell@wisc.edu

scan1pattern function