Package: ggmanh 1.17.0

John Lee

ggmanh: Visualization Tool for GWAS Result

Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

Authors:John Lee [aut, cre], John Lee [aut], Xiuwen Zheng [ctb, dtc]

ggmanh_1.17.0.tar.gz
ggmanh_1.17.0.zip(r-4.7)ggmanh_1.17.0.zip(r-4.6)ggmanh_1.17.0.zip(r-4.5)
ggmanh_1.17.0.tgz(r-4.6-any)ggmanh_1.17.0.tgz(r-4.5-any)
ggmanh_1.17.0.tar.gz(r-4.7-any)ggmanh_1.17.0.tar.gz(r-4.6-any)
ggmanh_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggmanh/json (API)

# Install 'ggmanh' in R:

install.packages('ggmanh', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ggmanh-1.17.0(bioc 3.24)ggmanh-1.16.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualization genomewideassociation genetics

3.97 score 47 scripts 10 exports 51 dependencies

Last updated from:43f0523906. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	218
linux-devel-x86_64	NOTE	244
source / vignettes	OK	203
linux-release-x86_64	NOTE	211
macos-release-arm64	NOTE	86
macos-oldrel-arm64	NOTE	90
windows-devel	NOTE	96
windows-release	NOTE	109
windows-oldrel	NOTE	94
wasm-release	OK	171

Exports:binned_manhattan_plot binned_manhattan_preprocess calc_new_pos default_gds_path gds_annotate manhattan_data_preprocess manhattan_plot manhattan_plot.default qqunif thinPoints

Dependencies:BiocGenerics Biostrings cli colorspace cpp11 crayon dichromat digest dplyr farver gdsfmt generics GenomicRanges ggplot2 ggrepel glue gtable IRanges isoband labeling lifecycle magrittr mapproj maps paletteer pals pillar pkgconfig prismatic purrr R6 RColorBrewer Rcpp rematch2 rlang rstudioapi S4Vectors S7 scales SeqArray Seqinfo stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

Guide to ggmanh Package

Rendered fromggmanh.Rmdusingknitr::rmarkdown

Last update: 2024-09-19
Started: 2021-09-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot Binned Manhattan Plot	binned_manhattan_plot binned_manhattan_plot,GRanges-method binned_manhattan_plot.data.frame binned_manhattan_plot.default binned_manhattan_plot.MPdataBinned
Preprocess GWAS Result for Binned Manhattan Plot	binned_manhattan_preprocess binned_manhattan_preprocess,GRanges-method binned_manhattan_preprocess.data.frame binned_manhattan_preprocess.default binned_manhattan_preprocess.MPdata
Calculate new x-position of each point	calc_new_pos
Path to Default GDS File	default_gds_path
Annotation with GDS File	gds_annotate
ggmanh: A package for visualization of GWAS results.	ggmanh
gnomAD Variant Annotation in SeqArray Format	ggmanh_annotation_gds
Preprocess GWAS Result	manhattan_data_preprocess manhattan_data_preprocess,GRanges-method manhattan_data_preprocess.data.frame manhattan_data_preprocess.default
Manhattan Plotting	manhattan_plot manhattan_plot,GRanges-method manhattan_plot.data.frame manhattan_plot.default manhattan_plot.MPdata
Plot Quantile-Quantile Plot of p-values against uniform distribution.	qqunif
Thin Data Points	thinPoints