Real Data Tutorial

From real SNP data

Normally, the SNP data is stored in .vcf format, thus we use an real VCF file as example here.

The example of real SNP file is available here

I. Load real SNP data

First, we need to extract the effective SNP columns from the original VCF file

# Load original SNP data
library(interacCircos)
library(stringr)

SNP_data<-read.table("snpExample_random_from_1000G.vcf",sep = "\t")
SNP_data<-SNP_data[,c(1,2,8)]
colnames(SNP_data)<-c("chr","pos","value")
SNP_data$value<-as.integer(str_split_fixed(str_split_fixed(SNP_data$value,
 ";", 2)[,1],"=",2)[,2])

After processing, the SNP_data should looks like below:

chr pos value
1 70573281 9
1 167102542 1
1 238165263 1
2 52714177 1827
... ... ...

II. Construct a chromosome track

In order to load other functional tracks, users should first construct a chromosome track!

# Load original SNP data
library(interacCircos)
library(stringr)

SNP_data<-read.table("snpExample_random_from_1000G.vcf",sep = "\t")
SNP_data<-SNP_data[,c(1,2,8)]
colnames(SNP_data)<-c("chr","pos","value")
SNP_data$value<-as.integer(str_split_fixed(str_split_fixed(SNP_data$value,
 ";", 2)[,1],"=",2)[,2])

Circos()

III. Add a snp track

In order to add snp track, users should first constrct a CircosSNP() function and then load this track on Circos() function

# Load original SNP data
library(interacCircos)
library(stringr)

SNP_data<-read.table("snpExample_random_from_1000G.vcf",sep = "\t")
SNP_data<-SNP_data[,c(1,2,8)]
colnames(SNP_data)<-c("chr","pos","value")
SNP_data$value<-as.integer(str_split_fixed(str_split_fixed(SNP_data$value, ";", 2)[,1],"=",2)[,2])

SNP_track<-CircosSnp('SNP01', minRadius =150, maxRadius = 190, data = SNP_data,fillColor= "#9ACD32",
                                      circleSize= 2)

Circos(moduleList = SNP_track)

IV. Add a background track

It's not pretty enough when only add a snp track, users can add other tracks to increase readability. 

# Load original SNP data
library(interacCircos)
library(stringr)

SNP_data<-read.table("snpExample_random_from_1000G.vcf",sep = "\t")
SNP_data<-SNP_data[,c(1,2,8)]
colnames(SNP_data)<-c("chr","pos","value")
SNP_data$value<-as.integer(str_split_fixed(str_split_fixed(SNP_data$value, ";", 2)[,1],"=",2)[,2])

SNP_track<-CircosSnp('SNP01', minRadius =150, maxRadius = 190, data = SNP_data,fillColor= "#9ACD32",
                                      circleSize= 2)
Bg_track<-CircosBackground('BG01',minRadius = 145, maxRadius = 200)

Circos(moduleList = SNP_track+Bg_track)

V. Add animation for tracks

As you know, interacCircos is interactive as it can add animation and mouse event to plot. Here, we add a mouse move event and a opening animation for snp track

# Load original SNP data
library(interacCircos)
library(stringr)

SNP_data<-read.table("snpExample_random_from_1000G.vcf",sep = "\t")
SNP_data<-SNP_data[,c(1,2,8)]
colnames(SNP_data)<-c("chr","pos","value")
SNP_data$value<-as.integer(str_split_fixed(str_split_fixed(SNP_data$value, ";", 2)[,1],"=",2)[,2])

SNP_track<-CircosSnp('SNP01', minRadius =150, maxRadius = 190, data = SNP_data,fillColor= "#9ACD32",
                                      circleSize= 2, animationDisplay =TRUE,animationTime= 2000,animationDelay= 0,
                                      animationType= "linear")
Bg_track<-CircosBackground('BG01',minRadius = 145, maxRadius = 200)

Circos(moduleList = SNP_track+Bg_track,SNPMouseEvent = TRUE,SNPMouseOverDisplay = TRUE,
SNPMouseOverTooltipsSetting = "style1",SNPMouseOutDisplay = TRUE,SNPMouseOutColor = NULL)