Dear all,

please could I have some (introductory) information about the CIRCULAR DISPLAY in GGBIO is setup; especially function on 1) seqlength and 2) radius;

the following 2 examples give very different displays; thanks !

<> example 1 :

gr <- GRanges("chr21", strand="+", IRanges(start = c(1, 100), end = c(10, 200)), score = c(10,20))

seqlengths(gr) <- c("chr21"=100000)

ggplot() + layout_circle(gr, geom = "bar", radius = 100, trackWidth = 4, aes(fill = factor(score), y = score))

<> example 2 :

gr <- GRanges("chr21", strand="+", IRanges(start = c(1, 100), end = c(10, 200)), score = c(10,20))

seqlengths(gr) <- max(end(gr))-min(start(gr))

ggplot() + layout_circle(gr, geom = "bar", radius = 100, trackWidth = 4, aes(fill = factor(score), y = score))

When you make a plot of a 200 bp region on a circular chromosome that is 100,000 bp long (e.g., you are plotting 0.2% of the genome), it's like you zoomed in on a very small region of a big circle. At that point it looks linear because the curvature is so slight (just like the earth looks flat to us when on the surface). But if the region you are plotting is a large portion of the (circular) genome, then it's as if you zoomed out, and can now see the circularity.

gr <- GRanges("chr21", strand="+", IRanges(start = c(1, 100), end = c(10, 200)), score = c(10,20))

fun <- function(gr, sq){
 seqlengths(gr) <- sq
 ggplot() + layout_circle(gr, geom = "bar", radius = 100, trackWidth = 4, aes(fill = factor(score), y = score))
 }

sqlst <- c(200, 500, 800, 1000, 2000, 5000)

pdf("tmp.pdf")

lapply(sqlst, function(x) fun(gr, x))

dev.off()

And look at the pdf.

Thank you James for time and prompt help, really appreciate it ! It is a beautiful piece of R code ...  I may have some additional questions, as I am trying to plot also some gene tracks in the CIRCULAR format, together with interaction links ;) will get back to you later, shall you find 5 minutes ;) thanks a lot !

Oh, well, it looks that we would need to set up the seqlengths specifically for each GRanges object depending on the segment we would like to represent in order to scale everything accordingly :

for example :

gr1 <- GRanges("chr21", strand="+", IRanges(start = c(1, 20), end = c(10, 30)), score = c(0,20)) 

gr2 <- GRanges("chr21", strand="+", IRanges(start = c(1, 400), end = c(300, 600)), score = c(0,2000))

min_start_gr1 <- min(start(gr1))
min_start_gr2 <- min(start(gr2))

min_start_gr1_gr2 <- min(min_start_gr1, min_start_gr2)

max_end_gr1 <- max(end(gr1))
max_end_gr2 <- max(end(gr2))

max_end_gr1_gr2 <- max(max_end_gr1, max_end_gr2)

#####################################

seqlengths(gr1) <- max_end_gr1_gr2 - min_start_gr1_gr2
seqlengths(gr2) <- max_end_gr1_gr2 - min_start_gr1_gr2

ggplot() + layout_circle(gr2, geom = "bar", radius = 100, trackWidth = 4, aes(fill = score, y = score)) +
           layout_circle(gr2, geom = "point", color = "red", radius = 110, trackWidth = 3, grid = TRUE, aes(y = score)) +
           layout_circle(gr1, geom = "bar", radius = 120, trackWidth = 4, aes(fill = score, y = score)) +
           layout_circle(gr1, geom = "point", color = "red", radius = 130, trackWidth = 3, grid = TRUE, aes(y = score))