Package: qtl2ggplot 1.2.4

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:Brian S Yandell [aut, cre], Karl W Broman [aut]

qtl2ggplot_1.2.4.tar.gz
qtl2ggplot_1.2.4.zip(r-4.5)qtl2ggplot_1.2.4.zip(r-4.4)qtl2ggplot_1.2.4.zip(r-4.3)
qtl2ggplot_1.2.4.tgz(r-4.4-x86_64)qtl2ggplot_1.2.4.tgz(r-4.4-arm64)qtl2ggplot_1.2.4.tgz(r-4.3-x86_64)qtl2ggplot_1.2.4.tgz(r-4.3-arm64)
qtl2ggplot_1.2.4.tar.gz(r-4.5-noble)qtl2ggplot_1.2.4.tar.gz(r-4.4-noble)
qtl2ggplot_1.2.4.tgz(r-4.4-emscripten)qtl2ggplot_1.2.4.tgz(r-4.3-emscripten)
qtl2ggplot.pdf |qtl2ggplot.html✨
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/qtl2ggplot/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

4.20 score 5 stars 16 scripts 287 downloads 23 exports 53 dependencies

Last updated 8 months agofrom:310ad3b4e7. Checks:OK: 7 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 11 2024
R-4.5-win-x86_64	NOTE	Nov 11 2024
R-4.5-linux-x86_64	NOTE	Nov 11 2024
R-4.4-win-x86_64	OK	Nov 11 2024
R-4.4-mac-x86_64	OK	Nov 11 2024
R-4.4-mac-aarch64	OK	Nov 11 2024
R-4.3-win-x86_64	OK	Nov 11 2024
R-4.3-mac-x86_64	OK	Nov 11 2024
R-4.3-mac-aarch64	OK	Nov 11 2024

Exports:[.listof_scan1coef autoplot.genes autoplot.listof_scan1coef autoplot.scan1 autoplot.scan1coef ggplot_coef ggplot_coefCC ggplot_genes ggplot_listof_scan1coef ggplot_onegeno ggplot_peaks ggplot_pxg ggplot_scan1 ggplot_snpasso listof_scan1coef mean_pxg subset_listof_scan1coef subset.listof_scan1coef summary_listof_scan1coef summary_scan1 summary_scan1coef summary.scan1 summary.scan1coef

Dependencies:assertthat bit bit64 blob cachem cli colorspace cpp11 data.table DBI dplyr fansi farver fastmap generics ggplot2 ggrepel glue gtable isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix memoise mgcv munsell nlme pillar pkgconfig plogr purrr qtl2 R6 RColorBrewer Rcpp RcppEigen rlang RSQLite scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr yaml

R/qtl2ggplot Vignette

Brian S. Yandell

Rendered fromqtl2ggplot.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2021-07-17
Started: 2018-02-08

Citation

Development and contributors

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