codes/home_circos_ggplot_chiapet_intra.R
In andronekomimi/SNPVizualTools: Suite of R tools for custom SNP vizualisation
######################### ARGUMENTS ###############################
args <- commandArgs(trailingOnly = TRUE)
#
# if(length(args) < 5) {
# stop("Argument missing! Usage : scrip.R chrX start stop target_name path_to_snp_list [highlight_region fac. start:end]")
# }
#
#
# current_chr = args[1]
# current_start = as.numeric(args[2])
# current_stop = as.numeric(args[3])
# current_target = args[4]
# snps_list = args[5]
# current_chr = "10"
# current_start = 80710000
# current_stop = 80992000
# current_target = "ZMIZ1"
# snps_list = "~/Workspace/COLLAB/ZMIZ1_snps"
current_chr = "17"
current_start = 53000000
current_stop = 53500000
current_target = "COX11"
snps_list = "~/Workspace/COLLAB/COX11_snps"
######################### LOAD LIBRARY ###############################
suppressMessages(library(GenomicRanges))
suppressMessages(library(rtracklayer))
suppressMessages(library(ggbio))
######################### FUNCTIONS ###############################
produce_circos <- function(gr_left, gr_right, current_name, ideo, snps) {
seqlevels(gr_left) <- seqlevels(ideo)
seqlengths(gr_left) <- seqlengths(ideo)
seqlevels(gr_right) <- seqlevels(ideo)
seqlengths(gr_right) <- seqlengths(ideo)
values(gr_left)$to.gr <- gr_right
gr <- gr_left
seqlevels(snps) <- seqlevels(ideo)
seqlengths(snps) <- seqlengths(ideo)
# preparation affichage coord
coord_name = seq(from = start(current_range), to = end(current_range), by = 10000)
coord_pos = coord_name - start(current_range)
coord_range = IRanges(coord_pos, coord_pos)
coord_name = GRanges(seqnames = as.character(seqlevels(current_range)),
ranges = coord_range, label = coord_name)
p <- ggplot() +
layout_circle(ideo,
geom = "ideo",
radius = 36,
fill = "gray",
space.skip = 0,
trackWidth = 3)
p <- p + layout_circle(ideo,
geom = "ideo",
radius = 39,
fill = "black",
space.skip = 0,
trackWidth = 4)
p <- p + layout_circle(coord_name,
geom = "rect",
vjust = 0, radius = 43,
size = 0.1,
color = "black",
trackWidth = 0.5)
p <- p + layout_circle(coord_name,
geom = "text",
aes(label = label),
vjust = 0, radius = 44,
size = 1,
trackWidth = 0.5)
p <- p +
layout_circle(ideo,
geom = "scale",
size = 2,
radius = 36,
space.skip = 0,
scale.type = "B",
trackWidth = 3)
p <- p +
layout_circle(gr,
geom = "link",
linked.to = "to.gr",
#aes(color = color, alpha = 0.1, size = base_width),
aes(linetype = out_range),
color = "cyan4",
radius = 30,
space.skip = 0,
trackWidth = 0.5)
p <- p + ggtitle(current_name)
p <- p +
layout_circle(snps,
geom = "point",
aes(y = y, color = name),
grid = TRUE,
radius = 32,
size = 2,
space.skip = 0,
trackWidth = 4)
p
}
create_gr_from_df_4_circos_range = function(DF,label, current_range) {
chrom_start_idx = 1
left_start_idx = 2
chrom_end_idx = 4
right_start_idx = 5
left_end_idx = 3
right_end_idx = 6
chrom_start = c()
chrom_end = c()
left_start = c()
left_end = c()
right_start = c()
right_end = c()
base_width = c()
color = c()
out_range = c()
for (i in (1:nrow(DF)))
{
chrom_start_value = sub("chr","",DF[i,chrom_start_idx])
chrom_end_value = sub("chr","",DF[i,chrom_end_idx])
left_start_value = as.numeric(DF[i,left_start_idx])
left_end_value = as.numeric(DF[i,left_end_idx])
right_start_value = as.numeric(DF[i,right_start_idx])
right_end_value = as.numeric(DF[i,right_end_idx])
if(chrom_start_value == as.numeric(seqlevels(current_range)) && chrom_end_value == as.numeric(seqlevels(current_range))) {
if(left_end_value >= start(current_range) && right_start_value <= end(current_range))
{
chrom_start = c(chrom_start, chrom_start_value)
chrom_end = c(chrom_end, chrom_end_value)
left_start = c(left_start, transform_coord(left_start_value))
left_end = c(left_end, transform_coord(left_end_value))
right_start = c(right_start, transform_coord(right_start_value))
right_end = c(right_end, transform_coord(right_end_value))
base_width = c(base_width , left_end_value - left_start_value)
color = c(color,label)
out_range = c(out_range, FALSE)
}
else
{
if(chrom_start_value == as.numeric(seqlevels(current_range))) {
if((left_start_value >= start(current_range) && left_start_value <= end(current_range)) || (left_end_value >= start(current_range) && left_end_value <= end(current_range)))
{
chrom_start = c(chrom_start, chrom_start_value)
chrom_end = c(chrom_end, chrom_end_value)
left_start = c(left_start, transform_coord(left_start_value))
left_end = c(left_end, transform_coord(left_end_value))
right_start = c(right_start, transform_coord(right_start_value))
right_end = c(right_end, transform_coord(right_end_value))
base_width = c(base_width , left_end_value - left_start_value)
color = c(color,label)
out_range = c(out_range, TRUE)
}
}
else
{
if(chrom_end_value == as.numeric(seqlevels(current_range))) {
if((right_start_value >= start(current_range) && right_start_value <= end(current_range)) || (right_end_value >= start(current_range) && right_end_value <= end(current_range)))
{
chrom_start = c(chrom_start, chrom_start_value)
chrom_end = c(chrom_end, chrom_end_value)
left_start = c(left_start, transform_coord(left_start_value))
left_end = c(left_end, transform_coord(left_end_value))
right_start = c(right_start, transform_coord(right_start_value))
right_end = c(right_end, transform_coord(right_end_value))
base_width = c(base_width , left_end_value - left_start_value)
color = c(color,label)
out_range = c(out_range, TRUE)
}
}
}
}
}
}
out = list()
left_ranges = IRanges(left_start,left_end)
right_ranges = IRanges(right_start,right_end)
if(length(left_ranges) != 0) {
left_range <- GRanges(seqnames = chrom_start, ranges = left_ranges, base_width = base_width, color = color, out_range = out_range)
right_range <- GRanges(seqnames = chrom_end, ranges = right_ranges, base_width = base_width, color = color, out_range = out_range)
out = list(left_range, right_range)
}
out
}
transform_coord <- function(x) {
x - start(current_range)
}
###################### PROCESSIND ########################
###################### LOAD FILES #######################
############################ SINGAPORE DATA ############################
chiapet_k562_file1 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_lane13_chr", current_chr)
df1A <- read.table(chiapet_k562_file1, header=FALSE, stringsAsFactors=FALSE)
chiapet_k562_file2 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_lane24_chr", current_chr)
df2A <- read.table(chiapet_k562_file2, header=FALSE, stringsAsFactors=FALSE)
chiapet_mcf7_file3 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_lane11_chr", current_chr)
df3A <- read.table(chiapet_mcf7_file3, header=FALSE, stringsAsFactors=FALSE)
chiapet_mcf7_file4 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_lane23_chr", current_chr)
df4A <- read.table(chiapet_mcf7_file4, header=FALSE, stringsAsFactors=FALSE)
############################ STANFORD DATA ############################
chiapet_k562_file3 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_rep1_chr", current_chr)
df1B <- read.table(chiapet_k562_file3, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df1B[,4]), '[:,-]')
df1B = matrix(unlist(data), ncol = 7, byrow = TRUE)
chiapet_k562_file4 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_rep2_chr", current_chr)
df2B <- read.table(chiapet_k562_file4, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df2B[,4]), '[:,-]')
df2B = matrix(unlist(data), ncol = 7, byrow = TRUE)
chiapet_mcf7_file1 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_rep3_chr", current_chr)
df3B <- read.table(chiapet_mcf7_file1, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df3B[,4]), '[:,-]')
df3B = matrix(unlist(data), ncol = 7, byrow = TRUE)
chiapet_mcf7_file2 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_rep4_chr", current_chr)
df4B <- read.table(chiapet_mcf7_file2, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df4B[,4]), '[:,-]')
df4B = matrix(unlist(data), ncol = 7, byrow = TRUE)
snps_df <- read.table(snps_list, header=TRUE, stringsAsFactors=FALSE, quote = "\"", sep="\t")
print("Files loaded")
data("CRC", package = "biovizBase")
##################### CURRENT RANGE ###############################################
current_range <- IRanges(current_start,current_stop)
current_range <- GRanges(seqnames = current_chr, ranges = current_range)
current_range_length = end(current_range) - start(current_range)
##################### SNPS ###############################################
snps_df <- snps_df[order(snps_df$location),]
snp_ids <- snps_df$snp_id
snps_ranges <- IRanges(transform_coord(snps_df$location), transform_coord(snps_df$location))
snps <- GRanges(seqnames = current_chr, ranges = snps_ranges, imp = snps_df$metadata, y = seq(from = 1, to = length(snp_ids)), pos = snps_df$location)
snps$name <- snp_ids
###################### CREATE GENOMIC RANGES ######################
k562A_df = rbind(df1A,df2A)
mcf7A_df = rbind(df3A,df4A)
k562A = create_gr_from_df_4_circos_range(k562A_df,"K562 - ChIAPET", current_range)
mcf7A = create_gr_from_df_4_circos_range(mcf7A_df,"MCF7 - ChIAPET", current_range)
k562B_df = rbind(df1B,df2B)
mcf7B_df = rbind(df3B,df4B)
k562B = create_gr_from_df_4_circos_range(k562B_df,"K562 - ChIAPET", current_range)
mcf7B = create_gr_from_df_4_circos_range(mcf7B_df,"MCF7 - ChIAPET", current_range)
##################### CREATE IDEO ############################
ideo_current_range = hg19sub[as.numeric(current_chr)]
seqlevels(ideo_current_range) = as.character(unique(seqnames(ideo_current_range)))
start(ideo_current_range) = transform_coord(start(current_range))
end(ideo_current_range) = transform_coord(end(current_range))
seqlengths(ideo_current_range) = width(current_range)
ideo_current_chr = hg19sub[as.numeric(current_chr)]
seqlevels(ideo_current_chr) = as.character(unique(seqnames(ideo_current_chr)))
border = 100000
ideo_big_range = hg19sub[as.numeric(current_chr)]
seqlevels(ideo_big_range) = as.character(unique(seqnames(ideo_big_range)))
start(ideo_big_range) = transform_coord(start(current_range)) - border
end(ideo_big_range) = transform_coord(end(current_range)) + border
seqlengths(ideo_big_range) = width(ideo_big_range)
#################### RUN CIRCOS ##############################
# if(length(k562A) == 2) {
chiapet_k562A_on_range = suppressWarnings(produce_circos(k562A[[1]], k562A[[2]] , "ChIA-PET K562 - Singapore (range level)" , ideo_current_range , snps))
chiapet_k562A_on_range$plot$labels$colour = "SNP IDs"
# chiapet_k562_on_chr = suppressWarnings(produce_circos(k562A[[1]], k562A[[2]] , "ChIA-PET K562 - Singapore (chromosome level)" , ideo_current_chr , snps))
# chiapet_k562_on_chr$plot$labels$colour = "SNP IDs"
# }
#
# if(length(mcf7A) == 2) {
chiapet_mcf7A_on_range = suppressWarnings(produce_circos(mcf7A[[1]], mcf7A[[2]] , "ChIA-PET MCF7 - Singapore (range level)" , ideo_current_range , snps))
chiapet_mcf7A_on_range$plot$labels$colour = "SNP IDs"
# chiapet_mcf7_on_chr = suppressWarnings(produce_circos(mcf7A[[1]], mcf7A[[2]] , "ChIA-PET MCF7 - Singapore (chromosome level)" , ideo_current_chr , snps))
# chiapet_mcf7_on_chr$plot$labels$colour = "SNP IDs"
# }
#
# if(length(k562B) == 2) {
chiapet_k562B_on_range = suppressWarnings(produce_circos(k562B[[1]], k562B[[2]] , "ChIA-PET K562 - Stanford (range level)" , ideo_current_range , snps))
chiapet_k562B_on_range$plot$labels$colour = "SNP IDs"
# chiapet_k562_on_chr = suppressWarnings(produce_circos(k562B[[1]], k562B[[2]] , "ChIA-PET K562 - Stanford (chromosome level)" , ideo_current_chr , snps))
# chiapet_k562_on_chr$plot$labels$colour = "SNP IDs"
# }
#
# if(length(mcf7B) == 2) {
chiapet_mcf7B_on_range = suppressWarnings(produce_circos(mcf7B[[1]], mcf7B[[2]] , "ChIA-PET MCF7 - Stanford (range level)" , ideo_current_range , snps))
chiapet_mcf7B_on_range$plot$labels$colour = "SNP IDs"
# chiapet_mcf7_on_chr = suppressWarnings(produce_circos(mcf7B[[1]], mcf7B[[2]] , "ChIA-PET MCF7 - Stanford (chromosome level)" , ideo_current_chr , snps))
# chiapet_mcf7_on_chr$plot$labels$colour = "SNP IDs"
# }
andronekomimi/SNPVizualTools documentation built on May 10, 2019, 11:43 a.m.
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######################### ARGUMENTS ###############################
args <- commandArgs(trailingOnly = TRUE)
#
# if(length(args) < 5) {
# stop("Argument missing! Usage : scrip.R chrX start stop target_name path_to_snp_list [highlight_region fac. start:end]")
# }
#
#
# current_chr = args[1]
# current_start = as.numeric(args[2])
# current_stop = as.numeric(args[3])
# current_target = args[4]
# snps_list = args[5]
# current_chr = "10"
# current_start = 80710000
# current_stop = 80992000
# current_target = "ZMIZ1"
# snps_list = "~/Workspace/COLLAB/ZMIZ1_snps"
current_chr = "17"
current_start = 53000000
current_stop = 53500000
current_target = "COX11"
snps_list = "~/Workspace/COLLAB/COX11_snps"
######################### LOAD LIBRARY ###############################
suppressMessages(library(GenomicRanges))
suppressMessages(library(rtracklayer))
suppressMessages(library(ggbio))
######################### FUNCTIONS ###############################
produce_circos <- function(gr_left, gr_right, current_name, ideo, snps) {
seqlevels(gr_left) <- seqlevels(ideo)
seqlengths(gr_left) <- seqlengths(ideo)
seqlevels(gr_right) <- seqlevels(ideo)
seqlengths(gr_right) <- seqlengths(ideo)
values(gr_left)$to.gr <- gr_right
gr <- gr_left
seqlevels(snps) <- seqlevels(ideo)
seqlengths(snps) <- seqlengths(ideo)
# preparation affichage coord
coord_name = seq(from = start(current_range), to = end(current_range), by = 10000)
coord_pos = coord_name - start(current_range)
coord_range = IRanges(coord_pos, coord_pos)
coord_name = GRanges(seqnames = as.character(seqlevels(current_range)),
ranges = coord_range, label = coord_name)
p <- ggplot() +
layout_circle(ideo,
geom = "ideo",
radius = 36,
fill = "gray",
space.skip = 0,
trackWidth = 3)
p <- p + layout_circle(ideo,
geom = "ideo",
radius = 39,
fill = "black",
space.skip = 0,
trackWidth = 4)
p <- p + layout_circle(coord_name,
geom = "rect",
vjust = 0, radius = 43,
size = 0.1,
color = "black",
trackWidth = 0.5)
p <- p + layout_circle(coord_name,
geom = "text",
aes(label = label),
vjust = 0, radius = 44,
size = 1,
trackWidth = 0.5)
p <- p +
layout_circle(ideo,
geom = "scale",
size = 2,
radius = 36,
space.skip = 0,
scale.type = "B",
trackWidth = 3)
p <- p +
layout_circle(gr,
geom = "link",
linked.to = "to.gr",
#aes(color = color, alpha = 0.1, size = base_width),
aes(linetype = out_range),
color = "cyan4",
radius = 30,
space.skip = 0,
trackWidth = 0.5)
p <- p + ggtitle(current_name)
p <- p +
layout_circle(snps,
geom = "point",
aes(y = y, color = name),
grid = TRUE,
radius = 32,
size = 2,
space.skip = 0,
trackWidth = 4)
p
}
create_gr_from_df_4_circos_range = function(DF,label, current_range) {
chrom_start_idx = 1
left_start_idx = 2
chrom_end_idx = 4
right_start_idx = 5
left_end_idx = 3
right_end_idx = 6
chrom_start = c()
chrom_end = c()
left_start = c()
left_end = c()
right_start = c()
right_end = c()
base_width = c()
color = c()
out_range = c()
for (i in (1:nrow(DF)))
{
chrom_start_value = sub("chr","",DF[i,chrom_start_idx])
chrom_end_value = sub("chr","",DF[i,chrom_end_idx])
left_start_value = as.numeric(DF[i,left_start_idx])
left_end_value = as.numeric(DF[i,left_end_idx])
right_start_value = as.numeric(DF[i,right_start_idx])
right_end_value = as.numeric(DF[i,right_end_idx])
if(chrom_start_value == as.numeric(seqlevels(current_range)) && chrom_end_value == as.numeric(seqlevels(current_range))) {
if(left_end_value >= start(current_range) && right_start_value <= end(current_range))
{
chrom_start = c(chrom_start, chrom_start_value)
chrom_end = c(chrom_end, chrom_end_value)
left_start = c(left_start, transform_coord(left_start_value))
left_end = c(left_end, transform_coord(left_end_value))
right_start = c(right_start, transform_coord(right_start_value))
right_end = c(right_end, transform_coord(right_end_value))
base_width = c(base_width , left_end_value - left_start_value)
color = c(color,label)
out_range = c(out_range, FALSE)
}
else
{
if(chrom_start_value == as.numeric(seqlevels(current_range))) {
if((left_start_value >= start(current_range) && left_start_value <= end(current_range)) || (left_end_value >= start(current_range) && left_end_value <= end(current_range)))
{
chrom_start = c(chrom_start, chrom_start_value)
chrom_end = c(chrom_end, chrom_end_value)
left_start = c(left_start, transform_coord(left_start_value))
left_end = c(left_end, transform_coord(left_end_value))
right_start = c(right_start, transform_coord(right_start_value))
right_end = c(right_end, transform_coord(right_end_value))
base_width = c(base_width , left_end_value - left_start_value)
color = c(color,label)
out_range = c(out_range, TRUE)
}
}
else
{
if(chrom_end_value == as.numeric(seqlevels(current_range))) {
if((right_start_value >= start(current_range) && right_start_value <= end(current_range)) || (right_end_value >= start(current_range) && right_end_value <= end(current_range)))
{
chrom_start = c(chrom_start, chrom_start_value)
chrom_end = c(chrom_end, chrom_end_value)
left_start = c(left_start, transform_coord(left_start_value))
left_end = c(left_end, transform_coord(left_end_value))
right_start = c(right_start, transform_coord(right_start_value))
right_end = c(right_end, transform_coord(right_end_value))
base_width = c(base_width , left_end_value - left_start_value)
color = c(color,label)
out_range = c(out_range, TRUE)
}
}
}
}
}
}
out = list()
left_ranges = IRanges(left_start,left_end)
right_ranges = IRanges(right_start,right_end)
if(length(left_ranges) != 0) {
left_range <- GRanges(seqnames = chrom_start, ranges = left_ranges, base_width = base_width, color = color, out_range = out_range)
right_range <- GRanges(seqnames = chrom_end, ranges = right_ranges, base_width = base_width, color = color, out_range = out_range)
out = list(left_range, right_range)
}
out
}
transform_coord <- function(x) {
x - start(current_range)
}
###################### PROCESSIND ########################
###################### LOAD FILES #######################
############################ SINGAPORE DATA ############################
chiapet_k562_file1 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_lane13_chr", current_chr)
df1A <- read.table(chiapet_k562_file1, header=FALSE, stringsAsFactors=FALSE)
chiapet_k562_file2 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_lane24_chr", current_chr)
df2A <- read.table(chiapet_k562_file2, header=FALSE, stringsAsFactors=FALSE)
chiapet_mcf7_file3 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_lane11_chr", current_chr)
df3A <- read.table(chiapet_mcf7_file3, header=FALSE, stringsAsFactors=FALSE)
chiapet_mcf7_file4 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_lane23_chr", current_chr)
df4A <- read.table(chiapet_mcf7_file4, header=FALSE, stringsAsFactors=FALSE)
############################ STANFORD DATA ############################
chiapet_k562_file3 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_rep1_chr", current_chr)
df1B <- read.table(chiapet_k562_file3, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df1B[,4]), '[:,-]')
df1B = matrix(unlist(data), ncol = 7, byrow = TRUE)
chiapet_k562_file4 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_K562_rep2_chr", current_chr)
df2B <- read.table(chiapet_k562_file4, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df2B[,4]), '[:,-]')
df2B = matrix(unlist(data), ncol = 7, byrow = TRUE)
chiapet_mcf7_file1 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_rep3_chr", current_chr)
df3B <- read.table(chiapet_mcf7_file1, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df3B[,4]), '[:,-]')
df3B = matrix(unlist(data), ncol = 7, byrow = TRUE)
chiapet_mcf7_file2 <- paste0("/home/nekomimi/Workspace/SNPVIZU/data/chiapet/parsed/CHIAPET_MCF7_rep4_chr", current_chr)
df4B <- read.table(chiapet_mcf7_file2, header=FALSE, stringsAsFactors=FALSE)
data <- strsplit(gsub("\\.\\.", "-", df4B[,4]), '[:,-]')
df4B = matrix(unlist(data), ncol = 7, byrow = TRUE)
snps_df <- read.table(snps_list, header=TRUE, stringsAsFactors=FALSE, quote = "\"", sep="\t")
print("Files loaded")
data("CRC", package = "biovizBase")
##################### CURRENT RANGE ###############################################
current_range <- IRanges(current_start,current_stop)
current_range <- GRanges(seqnames = current_chr, ranges = current_range)
current_range_length = end(current_range) - start(current_range)
##################### SNPS ###############################################
snps_df <- snps_df[order(snps_df$location),]
snp_ids <- snps_df$snp_id
snps_ranges <- IRanges(transform_coord(snps_df$location), transform_coord(snps_df$location))
snps <- GRanges(seqnames = current_chr, ranges = snps_ranges, imp = snps_df$metadata, y = seq(from = 1, to = length(snp_ids)), pos = snps_df$location)
snps$name <- snp_ids
###################### CREATE GENOMIC RANGES ######################
k562A_df = rbind(df1A,df2A)
mcf7A_df = rbind(df3A,df4A)
k562A = create_gr_from_df_4_circos_range(k562A_df,"K562 - ChIAPET", current_range)
mcf7A = create_gr_from_df_4_circos_range(mcf7A_df,"MCF7 - ChIAPET", current_range)
k562B_df = rbind(df1B,df2B)
mcf7B_df = rbind(df3B,df4B)
k562B = create_gr_from_df_4_circos_range(k562B_df,"K562 - ChIAPET", current_range)
mcf7B = create_gr_from_df_4_circos_range(mcf7B_df,"MCF7 - ChIAPET", current_range)
##################### CREATE IDEO ############################
ideo_current_range = hg19sub[as.numeric(current_chr)]
seqlevels(ideo_current_range) = as.character(unique(seqnames(ideo_current_range)))
start(ideo_current_range) = transform_coord(start(current_range))
end(ideo_current_range) = transform_coord(end(current_range))
seqlengths(ideo_current_range) = width(current_range)
ideo_current_chr = hg19sub[as.numeric(current_chr)]
seqlevels(ideo_current_chr) = as.character(unique(seqnames(ideo_current_chr)))
border = 100000
ideo_big_range = hg19sub[as.numeric(current_chr)]
seqlevels(ideo_big_range) = as.character(unique(seqnames(ideo_big_range)))
start(ideo_big_range) = transform_coord(start(current_range)) - border
end(ideo_big_range) = transform_coord(end(current_range)) + border
seqlengths(ideo_big_range) = width(ideo_big_range)
#################### RUN CIRCOS ##############################
# if(length(k562A) == 2) {
chiapet_k562A_on_range = suppressWarnings(produce_circos(k562A[[1]], k562A[[2]] , "ChIA-PET K562 - Singapore (range level)" , ideo_current_range , snps))
chiapet_k562A_on_range$plot$labels$colour = "SNP IDs"
# chiapet_k562_on_chr = suppressWarnings(produce_circos(k562A[[1]], k562A[[2]] , "ChIA-PET K562 - Singapore (chromosome level)" , ideo_current_chr , snps))
# chiapet_k562_on_chr$plot$labels$colour = "SNP IDs"
# }
#
# if(length(mcf7A) == 2) {
chiapet_mcf7A_on_range = suppressWarnings(produce_circos(mcf7A[[1]], mcf7A[[2]] , "ChIA-PET MCF7 - Singapore (range level)" , ideo_current_range , snps))
chiapet_mcf7A_on_range$plot$labels$colour = "SNP IDs"
# chiapet_mcf7_on_chr = suppressWarnings(produce_circos(mcf7A[[1]], mcf7A[[2]] , "ChIA-PET MCF7 - Singapore (chromosome level)" , ideo_current_chr , snps))
# chiapet_mcf7_on_chr$plot$labels$colour = "SNP IDs"
# }
#
# if(length(k562B) == 2) {
chiapet_k562B_on_range = suppressWarnings(produce_circos(k562B[[1]], k562B[[2]] , "ChIA-PET K562 - Stanford (range level)" , ideo_current_range , snps))
chiapet_k562B_on_range$plot$labels$colour = "SNP IDs"
# chiapet_k562_on_chr = suppressWarnings(produce_circos(k562B[[1]], k562B[[2]] , "ChIA-PET K562 - Stanford (chromosome level)" , ideo_current_chr , snps))
# chiapet_k562_on_chr$plot$labels$colour = "SNP IDs"
# }
#
# if(length(mcf7B) == 2) {
chiapet_mcf7B_on_range = suppressWarnings(produce_circos(mcf7B[[1]], mcf7B[[2]] , "ChIA-PET MCF7 - Stanford (range level)" , ideo_current_range , snps))
chiapet_mcf7B_on_range$plot$labels$colour = "SNP IDs"
# chiapet_mcf7_on_chr = suppressWarnings(produce_circos(mcf7B[[1]], mcf7B[[2]] , "ChIA-PET MCF7 - Stanford (chromosome level)" , ideo_current_chr , snps))
# chiapet_mcf7_on_chr$plot$labels$colour = "SNP IDs"
# }
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