| Type: | Package |
| Title: | Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms |
| Version: | 0.2.2 |
| Maintainer: | Zhaodong Hao <haozd1992@163.com> |
| Description: | 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. |
| License: | Artistic-2.0 |
| Encoding: | UTF-8 |
| LazyData: | true |
| Depends: | R (≥ 3.5.0) |
| Imports: | ggplot2, grDevices, grImport2, rsvg, scales, tools, tidyr, utils |
| RoxygenNote: | 6.1.1 |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2020-01-20 10:43:48 UTC; haozhaodong |
| Author: | Zhaodong Hao [aut, cre], Dekang Lv [aut], Ying Ge [aut], Jisen Shi [aut], Weijers Dolf [aut], Guangchuang Yu [aut], Jinhui Chen [aut] |
| Repository: | CRAN |
| Date/Publication: | 2020-01-20 11:20:02 UTC |
Fst between two Liriodendron groups
Description
Fst values between China east and west groups of Liriodendron chinense and being calculated in a 2-Mb sliding window with a 1-Mb step
Usage
data(Fst_between_CE_and_CW)Format
data frame
Source
Nature Plants, doi: 10.1038/s41477-018-0323-6
GFFex
Description
extract some specific feature information from a gff file
Usage
GFFex(input, karyotype, feature = "gene", window = 1e+06)
Arguments
input |
gff file |
karyotype |
karyotype file |
feature |
feature name |
window |
window size |
Value
dataframe
Author(s)
Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, Jinhui Chen
LTR distribution across the human genome
Description
LTR numbers was counted with a window of 1 Mb
Usage
data(LTR_density)Format
data frame
Source
UCSC (http://genome.ucsc.edu/index.html)
Pi of one Liriodendron group
Description
Pi values of the China east group of Liriodendron chinense and being calculated in a 2-Mb sliding window with a 1-Mb step
Usage
data(Pi_for_CE)Format
data frame
Source
Nature Plants, doi: 10.1038/s41477-018-0323-6
Pi of two Liriodendron groups
Description
Pi values of the China east and west groups of Liriodendron chinense and being calculated in a 2-Mb sliding window with a 1-Mb step
Usage
data(Pi_for_CE_and_CW)Format
data frame
Source
Nature Plants, doi: 10.1038/s41477-018-0323-6
500 RNAs' position
Description
500 RNAs randomly selected from all tRNAs, rRNAs and miRNA in the human genome.
Usage
data(Random_RNAs_500)Format
data frame
Source
Gencode (https://www.gencodegenes.org/)
convertSVG
Description
convert svg to png or other format
Usage
convertSVG(svg, file = "chromosome", device = NULL, width = 8.2677,
height = 11.6929, dpi = 300)
svg2pdf(svg, file = "chromosome", width = 8.2677, height = 11.6929,
dpi = 300)
svg2png(svg, file = "chromosome", width = 8.2677, height = 11.6929,
dpi = 300)
svg2tiff(svg, file = "chromosome", width = 8.2677, height = 11.6929,
dpi = 300)
svg2jpg(svg, file = "chromosome", width = 8.2677, height = 11.6929,
dpi = 300)
Arguments
svg |
svg file |
file |
output file name |
device |
target format |
width |
output width |
height |
output height |
dpi |
output dpi |
Value
invisible grob object
Author(s)
Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, Jinhui Chen
Gene distribution across the human genome
Description
Gene numbers was counted with a window of 1 Mb
Usage
data(gene_density)Format
data frame
Source
Gencode (https://www.gencodegenes.org/)
Karyotype information of the human genome
Description
The version of this geome is gencode.v29.
Usage
data(human_karyotype)Format
data frame
Source
Gencode (https://www.gencodegenes.org/)
ideogram
Description
ideogram with overlaid heatmap annotation and optional track label
Usage
ideogram(karyotype, overlaid = NULL, label = NULL, label_type = NULL,
synteny = NULL, colorset1 = c("#4575b4", "#ffffbf", "#d73027"),
colorset2 = c("#b35806", "#f7f7f7", "#542788"), width = 170,
Lx = 160, Ly = 35, output = "chromosome.svg")
Arguments
karyotype |
karyotype data |
overlaid |
overlaid data |
label |
track label data |
label_type |
track label type, only support four types: marker, heatmap, line and polygon |
synteny |
synteny data |
colorset1 |
overlaid heatmap color |
colorset2 |
label heatmap color |
width |
width of plot region |
Lx |
position of legend (x) |
Ly |
position of legend (y) |
output |
output file, only svg is supported |
Value
output file
Author(s)
Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, Jinhui Chen
Examples
# Loading the package
require(RIdeogram)
# Loading the testing data
data(human_karyotype, package="RIdeogram")
data(gene_density, package="RIdeogram")
data(Random_RNAs_500, package="RIdeogram")
# Checking the data format
head(human_karyotype)
head(gene_density)
head(Random_RNAs_500)
# Running the function (Remove "#" before you run the following codes)
# ideogram(karyotype = human_karyotype)
# convertSVG("chromosome.svg", device = "png")
# Then, you will find a SVG file and a PNG file in your Working Directory.
Karyotype for two genome comparison
Description
Grape and Populus genomes
Usage
data(karyotype_dual_comparison)Format
data frame
Source
MCscan
Karyotype for three genome comparison
Description
Amborella, Grape and Liriodendron genomes
Usage
data(karyotype_ternary_comparison)Format
data frame
Source
MCscan
Karyotype information of the Liriodendron genome
Description
Liriodendron chinense genome
Usage
data(liriodendron_karyotype)Format
data frame
Source
Nature Plants, doi: 10.1038/s41477-018-0323-6
Synteny for two genome comparison
Description
Genome Synteny between Grape and Populus
Usage
data(synteny_dual_comparison)Format
data frame
Source
MCscan
Synteny for three genome comparison
Description
Genome Synteny among Amborella, Grape and Liriodendron
Usage
data(synteny_ternary_comparison)Format
data frame
Source
MCscan
Synteny for three genome comparison with gradient fill
Description
Genome Synteny among Amborella, Grape and Liriodendron with gradient fill
Usage
data(synteny_ternary_comparison_graident)Format
data frame
Source
MCscan