Closed mah238 closed 5 months ago
Hi folks, any help with the below would be great!
library(circlize) library(tidyr) library(dplyr)
read in bed files and chr info
ce11.chrominfo <- read.chromInfo(species = "ce11")$df ce11.blacklist <- read.table("~/ce11-blacklist.bed") exp041.blacklist <- read.table("~/exp041_regions.bed")
format chrominfo
ce11.chrominfo$numeric_column <- seq_along(ce11.chrominfo$chr) circos.genomicInitialize(ce11.chrominfo)
regions i want to plot
head(exp041.blacklist) chr start end merged numeric_column 1 I 3791 3990 0.6699761 1 2 I 108248 108447 0.4364079 2 3 I 229262 229461 0.4780256 3 4 I 299759 299958 0.5817262 4 5 I 433607 433806 1.8433321 5 6 I 518568 518767 0.6194894 6 circos.genomicTrackPlotRegion(exp041.blacklist, ylim = c(0, 5), panel.fun = function(region, value, ...) { circos.genomicLines(region, value, type = "segment", lwd = 2, ...) })
head(exp041.blacklist) chr start end merged numeric_column 1 I 3791 3990 0.6699761 1 2 I 108248 108447 0.4364079 2 3 I 229262 229461 0.4780256 3 4 I 299759 299958 0.5817262 4 5 I 433607 433806 1.8433321 5 6 I 518568 518767 0.6194894 6
circos.genomicTrackPlotRegion(exp041.blacklist, ylim = c(0, 5), panel.fun = function(region, value, ...) { circos.genomicLines(region, value, type = "segment", lwd = 2, ...) })
this simply creates another ring inside the inital circos plot without adding any annotation of where they are.
Hi folks, any help with the below would be great!
library(circlize) library(tidyr) library(dplyr)
read in bed files and chr info
format chrominfo
regions i want to plot
this simply creates another ring inside the inital circos plot without adding any annotation of where they are.