RIdeogram v0.2.0
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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.
Readme
RIdeogram: Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms
RIdeogram is a R package to draw SVG graphics to visualize and map genome-wide data on idiograms (Scalable Vector Graphics http://tutorials.jenkov.com/svg/index.html).
Installation
To install package from Github, you need to install the devtools package first
install.packages("devtools")
library(devtools)
Then, you can install the package RIdeogram
devtools::install_github('TickingClock1992/RIdeogram')
To install the package RIdeogram from CRAN
install.package("RIdeogram")
Citation
Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, and Jinhui Chen (2019). RIdeogram: Drawing SVG graphics to visualize and map genome-wide data on idiograms. R package version 0.2.0.
Usage
https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html
Maintainer
Zhaodong Hao haozd1992@163.com
Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China
College of Forestry, Nanjing Forestry University
Nanjing 210037, China
https://github.com/TickingClock1992
THANKS
Welcome to any suggestions and discussions.
Functions in RIdeogram
| Name | Description | |
| Pi_for_CE_and_CW | Pi of two Liriodendron groups | |
| karyotype_dual_comparison | Karyotype for two genome comparison | |
| Random_RNAs_500 | 500 RNAs' position | |
| karyotype_ternary_comparison | Karyotype for three genome comparison | |
| synteny_dual_comparison | Synteny for two genome comparison | |
| liriodendron_karyotype | Karyotype information of the Liriodendron genome | |
| LTR_density | LTR distribution across the human genome | |
| Pi_for_CE | Pi of one Liriodendron group | |
| Fst_between_CE_and_CW | Fst between two Liriodendron groups | |
| GFFex | GFFex | |
| synteny_ternary_comparison | Synteny for three genome comparison | |
| synteny_ternary_comparison_graident | Synteny for three genome comparison with gradient fill | |
| gene_density | Gene distribution across the human genome | |
| convertSVG | convertSVG | |
| ideogram | ideogram | |
| human_karyotype | Karyotype information of the human genome | |
| No Results! | ||
Vignettes of RIdeogram
Last month downloads
Details
| Type | Package |
| License | Artistic-2.0 |
| Encoding | UTF-8 |
| LazyData | true |
| RoxygenNote | 6.1.1 |
| VignetteBuilder | knitr |
| NeedsCompilation | no |
| Packaged | 2019-11-08 14:38:45 UTC; haozhaodong |
| Repository | CRAN |
| Date/Publication | 2019-11-08 15:00:02 UTC |
| imports | ggplot2 , grDevices , grImport2 , rsvg , scales , tidyr , tools , utils |
| suggests | knitr , rmarkdown |
| depends | R (>= 3.5.0) |
| Contributors | Guangchuang Yu, Dekang Lv, Ying Ge, Jisen Shi, Jinhui Chen, Weijers Dolf |
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