ideogram: ideogram

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

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.

RIdeogram documentation built on Jan. 20, 2020, 5:07 p.m.