ideogram {RIdeogram}

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.