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Generate a circosplot for a bacterial genome + map other stuffs

Open BioRB opened this issue 3 years ago • 0 comments

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: Screenshot from 2022-11-02 15-10-30strap

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

BioRB avatar Nov 02 '22 14:11 BioRB