Add warning when chromosome in track is not defined in genome

[koalive]

I'm using BioCircos with the short script here attached. I wanted to contact you because the SNP track does not appear on the output graph and I couldn't find any reasons why. First, I set the chromosom number and length. Then I put a Background track in the object "tracklist". It's working so far. But when I add BioCircosSNPTrack, there is no difference in the output, like if I didn't add anything. Could you please help me with this problem ?

Shortened script:

library("BioCircos")
myGenome = list("A1"= 59.94, "A2" = 74.9, "A3" = 84.1,
                "A4" = 45.63, "A5" = 72.67, "A6" = 75.02, 
                "A7" = 53.76, "A8" = 54.79, "A9" = 98.81,
                "A10" = 51.8, "C1" = 54.99, "C2" = 70.61, 
                "C3" = 104.07, "C4" = 88.17, "C5" = 84.18, 
                "C6" = 60.23, "C7" = 63.12, "C8" = 69.55,
                "C9" = 75.3)

tracklist = BioCircosBackgroundTrack("myBackgroundTrack", 
	minRadius = 0.9, 
	maxRadius=0.9, 
	borderColors="#AAAAAA", 
	borderSize=0.6, 
	fillColors="#BBBBBB") + 
	BioCircosBackgroundTrack("myBackgroundTrack", 
		minRadius = 0.8, 
		maxRadius=0.8, 
		borderColors="#AAAAAA", 
		borderSize=0.6, 
		fillColors="#BBBBBB")
points_chromosomesLPR = c('A2', 'A5', 'A6', 'A07', 'C8', 'C9')
points_coordinatesLPR = c(14.8, 48.3, 4, 47.4, 64, 2.7)
points_values = 0:1
tracklist = tracklist + BioCircosSNPTrack('mySNPTrack', 
	points_chromosomesLPR, 
	points_coordinatesLPR, 
	points_values, 
	colors=c("black"), 
	minRadius = 0.8, 
	maxRadius = 0.9, 
	size = 2) 

BioCircos(tracklist, genome = myGenome, geomeFillColor = c("red"), 
	genomeTicksDisplay = TRUE, genomeLabelTextSize = "14pt")

Dear X,

It seems the main issue is a typo when you define the chromosome list for your SNP track (you didn't define the "A07" chromosome in points_chromosomesLPR, so I assume you meant "A7"). If I correct that and call BioCircos again, the SNPs are displayed correctly. I guess adding a warning to the package when the chromosome is not defined would help avoiding these errors, so I'll add that as a suggestion on Github. Cheers,

Loan