Dear Developers,
I'm trying to use your script to map methylation positions on a bacterial genome of 4M bp, but something is going wrong because in the end I obtain an empty plot.
Here what I do:
library(BioCircos) myGenome = list ("Bacterial" = 4000000) BioCircos(genome = myGenome, genomeFillColor = c("Reds"), chrPad = 0, genomeLabelDy = 25, genomeTicksScale = 4e+4) csv <- read.csv("file.csv", sep="\t", header = FALSE) points_chromosomes = c("chromosome_1") points_coordinates <- csv$V2 points_values <- csv$V5 tracklist = BioCircosSNPTrack('mySNPTrack', points_chromosomes, points_coordinates, points_values, colors = c("tomato2", "tomato2"), minRadius = 0.5, maxRadius = 0.9) BioCircos(tracklist, genome = myGenome, genomeFillColor= c("tomato2", "darkblue"), chrPad = 0.02, displayGenomeBorder = FALSE, genomeTicksDisplay = FALSE, genomeLabelTextSize = 0)
I get an empty orange circle in the end. no methylation circle inside. no methylation positions.
the 2 column that i use for points_coordinates and points_values look like this:
basically I need 1 circle reppresening the bacterial genome and another inside for the methylation. I have a file with 2 columns, 1 for the genomic position and the other for the level of methylation.
thank a lot!
Best,
RB
Dear Developers,
I'm trying to use your script to map methylation positions on a bacterial genome of 4M bp, but something is going wrong because in the end I obtain an empty plot.
Here what I do:
library(BioCircos) myGenome = list ("Bacterial" = 4000000) BioCircos(genome = myGenome, genomeFillColor = c("Reds"), chrPad = 0, genomeLabelDy = 25, genomeTicksScale = 4e+4) csv <- read.csv("file.csv", sep="\t", header = FALSE) points_chromosomes = c("chromosome_1") points_coordinates <- csv$V2 points_values <- csv$V5 tracklist = BioCircosSNPTrack('mySNPTrack', points_chromosomes, points_coordinates, points_values, colors = c("tomato2", "tomato2"), minRadius = 0.5, maxRadius = 0.9) BioCircos(tracklist, genome = myGenome, genomeFillColor= c("tomato2", "darkblue"), chrPad = 0.02, displayGenomeBorder = FALSE, genomeTicksDisplay = FALSE, genomeLabelTextSize = 0)I get an empty orange circle in the end. no methylation circle inside. no methylation positions.
the 2 column that i use for points_coordinates and points_values look like this:
basically I need 1 circle reppresening the bacterial genome and another inside for the methylation. I have a file with 2 columns, 1 for the genomic position and the other for the level of methylation.
thank a lot!
Best,
RB