Whole Genome Allele Scan | Genome Allele Scan for Chr 2 | Scan chromosome and summarize peak | Examine coefficients for the 8 alleles | SNP Association Mapping | Strain Distribution Pattern (SDP) Scan | Genes in Peak Region | Multiple Phenotypes | Genome scans for multile phenotypes | SNP scans for multiple phenotypes | SDP scans for multiple phenotypes | LOD peaks for multiple phenotypes | Coefficients for multiple phenotypes | Coefficients for 36 allele pairs
Package: qtl2ggplot 1.2.8
Brian S Yandell
qtl2ggplot: Data Visualization for QTL Experiments
Functions to plot QTL (quantitative trait loci) analysis results and related diagnostics. Part of 'qtl2', an upgrade of the 'qtl' package to better handle high-dimensional data and complex cross designs.
Authors:
qtl2ggplot_1.2.8.tar.gz
qtl2ggplot_1.2.8.zip(r-4.7)qtl2ggplot_1.2.8.zip(r-4.6)qtl2ggplot_1.2.8.zip(r-4.5)
qtl2ggplot_1.2.8.tgz(r-4.6-x86_64)qtl2ggplot_1.2.8.tgz(r-4.6-arm64)qtl2ggplot_1.2.8.tgz(r-4.5-x86_64)qtl2ggplot_1.2.8.tgz(r-4.5-arm64)
qtl2ggplot_1.2.8.tar.gz(r-4.7-arm64)qtl2ggplot_1.2.8.tar.gz(r-4.7-x86_64)qtl2ggplot_1.2.8.tar.gz(r-4.6-arm64)qtl2ggplot_1.2.8.tar.gz(r-4.6-x86_64)
qtl2ggplot_1.2.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
qtl2ggplot/json (API)
| # Install 'qtl2ggplot' in R: |
| install.packages('qtl2ggplot', repos = c('https://byandell-sysgen.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/byandell-sysgen/qtl2ggplot/issues
Last updated from:6869ce9b97. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 186 | ||
| linux-devel-x86_64 | OK | 193 | ||
| source / vignettes | OK | 267 | ||
| linux-release-arm64 | OK | 183 | ||
| linux-release-x86_64 | OK | 190 | ||
| macos-release-arm64 | OK | 152 | ||
| macos-release-x86_64 | OK | 183 | ||
| macos-oldrel-arm64 | OK | 157 | ||
| macos-oldrel-x86_64 | OK | 305 | ||
| windows-devel | OK | 147 | ||
| windows-release | OK | 155 | ||
| windows-oldrel | OK | 137 | ||
| wasm-release | OK | 169 |
Exports:[.listof_scan1coefautoplot.genesautoplot.listof_scan1coefautoplot.scan1autoplot.scan1coefggplot_coefggplot_coefCCggplot_genesggplot_listof_scan1coefggplot_onegenoggplot_peaksggplot_pxgggplot_scan1ggplot_snpassolistof_scan1coefmean_pxgsubset_listof_scan1coefsubset.listof_scan1coefsummary_listof_scan1coefsummary_scan1summary_scan1coefsummary.scan1summary.scan1coef
Dependencies:assertthatbitbit64blobcachemclicpp11data.tableDBIdplyrfarverfastmapgenericsggplot2ggrepelgluegtableisobandjsonlitelabelinglifecyclemagrittrmemoisepillarpkgconfigpurrrqtl2R6RColorBrewerRcppRcppEigenrlangRSQLiteS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Set up col, pattern and group for plotting. | color_patterns_get |
| Set up col, pattern, shape and group for plotting. | color_patterns_pheno |
| Set up colors for patterns or points | color_patterns_set |
| Plot QTL effects along chromosome | autoplot.scan1coef ggplot_coef ggplot_coefCC |
| Plot gene locations for a genomic interval | autoplot.genes ggplot_genes |
| GGPlot internal routine for ggplot_genes | ggplot_genes_internal |
| Plot of object of class listof_scan1coeff | autoplot.listof_scan1coef ggplot_listof_scan1coef |
| Plot one individual's genome-wide genotypes | ggplot_onegeno |
| Plot QTL peak locations | ggplot_peaks |
| Plot phenotype vs genotype | ggplot_pxg mean_pxg |
| Plot a genome scan | autoplot.scan1 ggplot_scan1 ggplot_scan1_internal |
| Plot SNP associations | ggplot_snpasso |
| List of scan1coef objects | listof_scan1coef subset.listof_scan1coef subset_listof_scan1coef summary.listof_scan1coef summary.scan1coef summary_listof_scan1coef summary_scan1coef [.listof_scan1coef |
| Convert sdp to pattern | sdp_to_pattern |
| Summary of scan1 object | summary.scan1 summary_scan1 |