Package: RIdeogram 0.2.2

RIdeogram: Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms

For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species.

Authors:Zhaodong Hao [aut, cre], Dekang Lv [aut], Ying Ge [aut], Jisen Shi [aut], Weijers Dolf [aut], Guangchuang Yu [aut], Jinhui Chen [aut]

RIdeogram_0.2.2.tar.gz
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RIdeogram.pdf |RIdeogram.html✨
RIdeogram/json (API)

# Install 'RIdeogram' in R:

install.packages('RIdeogram', repos = c('https://tickingclock1992.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tickingclock1992/rideogram/issues

Datasets:

Fst_between_CE_and_CW - Fst between two Liriodendron groups
LTR_density - LTR distribution across the human genome
Pi_for_CE - Pi of one Liriodendron group
Pi_for_CE_and_CW - Pi of two Liriodendron groups
Random_RNAs_500 - 500 RNAs' position
gene_density - Gene distribution across the human genome
human_karyotype - Karyotype information of the human genome
karyotype_dual_comparison - Karyotype for two genome comparison
karyotype_ternary_comparison - Karyotype for three genome comparison
liriodendron_karyotype - Karyotype information of the Liriodendron genome
synteny_dual_comparison - Synteny for two genome comparison
synteny_ternary_comparison - Synteny for three genome comparison
synteny_ternary_comparison_graident - Synteny for three genome comparison with gradient fill

On CRAN:

7.98 score 170 stars 62 scripts 502 downloads 9 mentions 7 exports 42 dependencies

Last updated 5 years agofrom:aaaa2b303c. Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 31 2025
R-4.5-win	WARNING	Mar 31 2025
R-4.5-mac	WARNING	Mar 31 2025
R-4.5-linux	WARNING	Mar 31 2025
R-4.4-win	WARNING	Mar 31 2025
R-4.4-mac	WARNING	Mar 31 2025
R-4.4-linux	WARNING	Mar 31 2025
R-4.3-win	WARNING	Mar 31 2025
R-4.3-mac	WARNING	Mar 31 2025

Exports:convertSVG GFFex ideogram svg2jpg svg2pdf svg2png svg2tiff

Dependencies:base64enc cli colorspace cpp11 dplyr fansi farver generics ggplot2 glue grImport2 gtable isoband jpeg labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig png purrr R6 RColorBrewer rlang rsvg scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr XML

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on idiograms

Zhaodong Hao

Rendered fromRIdeogram.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2020-01-20
Started: 2018-12-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
convertSVG	convertSVG svg2jpg svg2pdf svg2png svg2tiff
Fst between two Liriodendron groups	Fst_between_CE_and_CW
Gene distribution across the human genome	gene_density
GFFex	GFFex
Karyotype information of the human genome	human_karyotype
ideogram	ideogram
Karyotype for two genome comparison	karyotype_dual_comparison
Karyotype for three genome comparison	karyotype_ternary_comparison
Karyotype information of the Liriodendron genome	liriodendron_karyotype
LTR distribution across the human genome	LTR_density
Pi of one Liriodendron group	Pi_for_CE
Pi of two Liriodendron groups	Pi_for_CE_and_CW
500 RNAs' position	Random_RNAs_500
Synteny for two genome comparison	synteny_dual_comparison
Synteny for three genome comparison	synteny_ternary_comparison
Synteny for three genome comparison with gradient fill	synteny_ternary_comparison_graident