functions.R
get.bedpe.chr2R = function(df,min.reads=10,min.dist=3000000){
require(Sushi)
#detach("package:dplyr", unload=TRUE)
#detach("package:plyr", unload=TRUE)
require(dplyr)
require(stringr)
chrom=2
chromstart=1
chromend=25286936
df = subset(df,df$V1==chrom)
df$dist = abs(df$V2-df$V5)
df = subset(df,df$dist>min.dist)
df$dist=NULL
bedpe = df
bedpe$V4 = ifelse(bedpe$V4=="=",bedpe$V1)
ex.data = data("Sushi_5C.bedpe")
#str(Sushi_5C.bedpe)
colnames(bedpe)=colnames(Sushi_5C.bedpe)[c(1:6)]
bedpe$name = NA
#head(bedpe)
# bedpe$score = log10(abs(bedpe$start1-bedpe$start2))
dfr1=bedpe
dfr1$distc = cut(bedpe$start1,include.lowest = TRUE,breaks = seq(1,chromend-200000,by = 100000))
dfr1 <- dfr1 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")),
end=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"[0-9-e+.]+$")),
mid=start+((end-start)/2))
dfr2=bedpe
dfr2$distc = cut(bedpe$start2,include.lowest = TRUE,breaks = seq(1,chromend,by = 100000))
dfr2 <- dfr2 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")),
end=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"[0-9-e+.]+$")),
mid=start+((end-start)/2))
bedpe$start1 = dfr1$start
bedpe$start2 = dfr2$start
bedpe$end1 = dfr1$end
bedpe$end2 = dfr2$end
head(bedpe)
bedpe2 = as.data.frame(bedpe %>% dplyr::group_by_all() %>% dplyr::summarise(score = n()))
head(bedpe2)
inv.coord = data.frame('start1'=c(14500000,8800000),"start2"=c(18700000,17700000))
inv2rns = data.frame('start1'=c(15300000),"start2"=c(20200000))
#fiveormoreeu = data.frame('start1' = c(5500000,12700000),'start2'=c(25100000,18900000))
smol = c(12700000,18900000)
# bedpe2$id = ifelse(bedpe2$start1 %in% inv.coord$start1 &
# bedpe2$start2 %in% inv.coord$start2,
# "In(2R)Mal",ifelse(bedpe2$start1<5300000,
# "heterochromatin","other"))
bedpe2$id = ifelse(bedpe2$start1 %in% inv.coord$start1 & bedpe2$start2 %in% inv.coord$start2,
"In(2R)Mal",
ifelse(bedpe2$start1 %in% inv2rns$start1 & bedpe2$start2 %in% inv2rns$start2,
"In(2R)NS", "unknown"))
bedpe2 = subset(bedpe2, bedpe2$score>min.reads)
return(bedpe2)
}
my.bedpe.plot.nreads.chr2R = function(dat,mytitle="Title"){
chrom=2
chromstart=1
chromend=25286936
dat = subset(dat,dat$chrom1==chrom & dat$chrom2==chrom)
dat$id2 = ifelse(dat$id=="In(2R)Mal",1,
ifelse(dat$id=="In(2R)NS",2,3))
str(dat)
# dat$id2 = if(length(unique(dat$id2))==1){
# runif(nrow(dat),min = 3,max = 4)
# } else {
# dat$id2
# }
str(dat)
# colores=ifelse(1%in%dat$id2, colorRampPalette(c("darkorange","grey")),
# ifelse(2%in%dat$id2, colorRampPalette(c("blue","grey")), colorRampPalette(c("grey","grey"))))
#
# colores
#
#colores
#plot.new()
try(
ifelse(
length(unique(dat$id2))==1,
plotBedpe(dat,
heights = dat$score,
chrom = '2',
chromstart = chromstart,
chromend = chromend,
plottype = 'ribbons'),
plotBedpe(dat,
heights = dat$score,
chrom = '2',
chromstart = chromstart,
chromend = chromend,
plottype = 'ribbons',
colorby = dat$id2,
colorbycol = topo.colors)
), silent=TRUE)
labelgenome(chrom = "2R", chromstart,chromend,n=50,scale="Mb")
#abline(v=c(14591034,18774475),col='black')
#abline(v=c(8855601,15616195),col='black',lty=6)
abline(v = c())
#legend("topright",inset=0.01,legend=c("In(2R)Mal","In(2R)NS","heterochromatin","unknown"),col=c(topo.colors(4)),pch=19,bty='n',text.font=2)
# legend("topright",legend = levels(as.factor(dat$id)),
# col = c(topo.colors(4)),
# pch=19,bty='n',text.font=2)
axis(side=2,las=2,tcl=.2)
title(mytitle)
}
get.bedpe.chr2L = function(df,min.reads=50,min.dist=3000000){
require(Sushi)
#detach("package:dplyr", unload=TRUE)
#detach("package:plyr", unload=TRUE)
require(dplyr)
require(stringr)
chrom='1'
chromstart=1
chromend=23513712
df = subset(df,df$V1==chrom)
df$dist = abs(df$V2-df$V5)
df = subset(df,df$dist>min.dist)
df$dist=NULL
bedpe = df
bedpe$V4 = ifelse(bedpe$V4=="=",bedpe$V1)
ex.data = data("Sushi_5C.bedpe")
#str(Sushi_5C.bedpe)
colnames(bedpe)=colnames(Sushi_5C.bedpe)[c(1:6)]
bedpe$name = NA
#head(bedpe)
# bedpe$score = log10(abs(bedpe$start1-bedpe$start2))
dfr1=bedpe
dfr1$distc = cut(bedpe$start1,include.lowest = TRUE,breaks = seq(1,chromend-200000,by = 100000))
dfr1 <- dfr1 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")),
end=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"[0-9-e+.]+$")),
mid=start+((end-start)/2))
dfr2=bedpe
dfr2$distc = cut(bedpe$start2,include.lowest = TRUE,breaks = seq(1,chromend,by = 100000))
dfr2 <- dfr2 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")),
end=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"[0-9-e+.]+$")),
mid=start+((end-start)/2))
bedpe$start1 = dfr1$start
bedpe$start2 = dfr2$start
bedpe$end1 = dfr1$end
bedpe$end2 = dfr2$end
head(bedpe)
bedpe2 = as.data.frame(bedpe %>% dplyr::group_by_all() %>% dplyr::summarise(score = n()))
head(bedpe2)
inv.coord = data.frame('start1'=c(2200000),"start2"=c(13100000))
#inv2rns = data.frame('start1'=c(15300000),"start2"=c(20200000))
#fiveormoreeu = data.frame('start1' = c(5500000,12700000),'start2'=c(25100000,18900000))
smol = c(12700000,18900000)
# bedpe2$id = ifelse(bedpe2$start1 %in% inv.coord$start1 &
# bedpe2$start2 %in% inv.coord$start2,
# "In(2R)Mal",ifelse(bedpe2$start1<5300000,
# "heterochromatin","other"))
bedpe2$id = ifelse(bedpe2$start1 %in% inv.coord$start1 & bedpe2$start2 %in% inv.coord$start2,
"In(2L)t", "unknown")
bedpe2 = subset(bedpe2, bedpe2$score>min.reads)
bedpe2
return(bedpe2)
}
my.bedpe.plot.nreads.chr2L = function(dat,mytitle="Title"){
chrom='1'
chromstart=1
chromend=23513712
dat = subset(dat,dat$chrom1==chrom & dat$chrom2==chrom)
dat$id2 = ifelse(dat$id=="In(2L)t",1,2)
dat
# dat$id2 = if(length(unique(dat$id2))==1){
# runif(nrow(dat),min = 3,max = 4)
# } else {
# dat$id2
# }
#
# dat
#colores=ifelse(1%in%dat$id2, colorRampPalette(c("blue","grey")), colorRampPalette(c("grey","grey")))
#dat
#colores
#plot.new()
try(ifelse(
length(unique(dat$id2))==1,
plotBedpe(dat,
heights = dat$score,
chrom = '1',
chromstart = chromstart,
chromend = chromend,
plottype = 'ribbons'),
plotBedpe(dat,
heights = dat$score,
chrom = '1',
chromstart = chromstart,
chromend = chromend,
plottype = 'ribbons',
colorby = dat$id2,
colorbycol = topo.colors)
),
silent=TRUE)
labelgenome(chrom = "2L", chromstart,chromend,n=50,scale="Mb")
#abline(v=c(14591034,18774475),col='black')
#abline(v=c(8855601,15616195),col='black',lty=6)
#legend("topright",inset=0.01,legend=c("In(2R)Mal","In(2R)NS","heterochromatin","unknown"),col=c(topo.colors(4)),pch=19,bty='n',text.font=2)
# legend("topright",legend = levels(as.factor(dat$id)),
# col = c(topo.colors(4)),
# pch=19,bty='n',text.font=2)
axis(side=2,las=2,tcl=.2)
title(mytitle)
}
get.bedpe.Sd = function(df,min.reads=1,min.dist=3000){
require(Sushi)
#detach("package:dplyr", unload=TRUE)
#detach("package:plyr", unload=TRUE)
require(dplyr)
require(stringr)
df = subset(df,df$V1==1)
df$dist = abs(df$V2-df$V5)
df = subset(df,df$dist>min.dist)
df$dist=NULL
bedpe = df
bedpe$V4 = ifelse(bedpe$V4=="=",bedpe$V1)
ex.data = data("Sushi_5C.bedpe")
#str(Sushi_5C.bedpe)
colnames(bedpe)=colnames(Sushi_5C.bedpe)[c(1:6)]
bedpe$name = NA
#head(bedpe)
# bedpe$score = log10(abs(bedpe$start1-bedpe$start2))
dfr1=bedpe
dfr1$distc = cut(bedpe$start1,include.lowest = TRUE,breaks = seq(19400000,19600000,by = 500))
dfr1 <- dfr1 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")),
end=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"[0-9-e+.]+$")),
mid=start+((end-start)/2))
dfr2=bedpe
dfr2$distc = cut(bedpe$start2,include.lowest = TRUE,breaks = seq(19400000,19600000,by = 500))
dfr2 <- dfr2 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")),
end=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"[0-9-e+.]+$")),
mid=start+((end-start)/2))
bedpe$start1 = dfr1$start
bedpe$start2 = dfr2$start
bedpe$end1 = dfr1$end
bedpe$end2 = dfr2$end
head(bedpe)
bedpe2 = as.data.frame(bedpe %>% dplyr::group_by_all() %>% dplyr::summarise(score = n()))
bedpe2$name ='unknown'
head(bedpe2)
bedpe2 = subset(bedpe2,bedpe2$score>min.reads)
bedpe2 = bedpe2[complete.cases(bedpe2),]
return(bedpe2)
}
my.bedpe.plot.Sd = function(dat,mytitle="Title"){
chrom='1'
chromstart=19430000
chromend=19460000
# pbpe = plotBedpe(dat,1,chromstart,chromend,heights = dat$score,
# plottype="loops",colorby=dat$score,colorbycol=SushiColors(3))
pbpe = plotBedpe(dat,1,chromstart,chromend,heights = dat$score,
plottype="loops")
labelgenome(chrom = "2L", chromstart,chromend,n=50,scale="bp")
abline(v=c(19441959,19447317),col='black',lty=6)
axis(side=2,las=2,tcl=.2)
title(mytitle)
}
