Package: ggmanh 1.11.0

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]

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ggmanh.pdf |ggmanh.html✨
ggmanh/json (API)
NEWS

# Install 'ggmanh' in R:

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

On BioConductor:ggmanh-1.11.0(bioc 3.21)ggmanh-1.10.0(bioc 3.20)

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

visualization genomewideassociation genetics

4.26 score 23 scripts 392 downloads 10 exports 66 dependencies

Last updated 5 months agofrom:c8acd632fd. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 29 2025
R-4.5-win	NOTE	Mar 29 2025
R-4.5-mac	NOTE	Mar 29 2025
R-4.5-linux	NOTE	Mar 29 2025
R-4.4-win	NOTE	Mar 29 2025
R-4.4-mac	NOTE	Mar 29 2025
R-4.4-linux	NOTE	Mar 29 2025
R-4.3-win	NOTE	Mar 29 2025
R-4.3-mac	NOTE	Mar 29 2025

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:askpass BiocGenerics Biostrings cli colorspace cpp11 crayon curl dichromat digest dplyr fansi farver gdsfmt generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr mapproj maps MASS Matrix mgcv mime munsell nlme openssl paletteer pals pillar pkgconfig prismatic purrr R6 RColorBrewer Rcpp rematch2 rlang rstudioapi S4Vectors scales SeqArray stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector

Guide to ggmanh Package

Rendered fromggmanh.Rmdusingknitr::rmarkdownon Mar 29 2025.

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