chromDraw (version 2.2.0)

chromDrawGR: Function chromDrawGR uses Genomic Ranges as input data format. This R function call the main C++ function.

Description

Function chromDrawGR uses Genomic Ranges as input data format. This R function call the main C++ function. If the output directory is not set, then it is use working directory for the outputs.

Usage

chromDrawGR(karyotypes, colors)

Arguments

karyotypes

vector of the Genomic Ranges structures per karyotype.

colors

data frame definition of coloros, containing color name and RGB of the color values.

Value

return exit state.

Examples

#load package
library(GenomicRanges)

#data generating
karyotype1 <- GRanges(seqnames =Rle(c("Ack1", "Ack2"), c(5, 5)),ranges = 
IRanges(start = c(0, 400000,0,3300000,6000000,0,2500000,0,3800000,6400000), 
        end = c(400000,3300000,0,6000000,10400000,2500000,3800000,0,6400000,14800000), 
        names = c("A","B","CENTROMERE","C","D","E","F","CENTROMERE","G","H")),  
        color = c("orange","yellow","","orange","red","green","green","","red","orange"));

karyotype2 <- GRanges(seqnames =Rle(c("Ack3", "Ack4"), c(4, 4)),ranges = 
IRanges(start = c(0,0, 2400000,3500000,0,0,2400000,6700000), 
        end = c(2400000,0,3500000,12200000,2400000,0,6700000,9200000), 
        names = c("I","CENTROMERE","J","K","L","CENTROMERE","M","N")), 
        color = c("light_blue","","orange","red","pink","","red","light_blue"));

inputData <- list(karyotype1,karyotype2);

#colors generating
name <- c("yellow", "red", "blue", "violet", "orange", "green", "light_blue", "pink");
r <- c(255, 255, 0, 255, 247, 0, 0, 230);
g <- c(255, 0, 0, 0 ,148, 255, 255, 170);
b <- c(0, 0, 255, 255, 29, 0, 255, 160);
inputColors <- data.frame(name,r,g,b);

#run the function with generated data and colors
chromDrawGR(inputData,inputColors);