The issue with the SNP-density plot

[ELPSYCONGRO977]

Thank you very much for developing this R package. However, I’ve recently encountered some issues while using it.
When I use a 2Mb interval for plotting, I ensure that my data contains at least one SNP in each bin, but the resulting plot still shows many gray bins：

The code I used is as follows:CMplot(data, plot.type = "d", bin.size = 2e6, col = c("darkgreen", "yellow", "red"), file = "tiff", dpi = 600, file.output = FALSE, verbose = TRUE)

To rule out issues caused by my personal operations, I used the pig60K example data and the corresponding example code for testing, but the results still did not meet expectations. I also conducted tests on other computers.

Looking forward to your answer！

[YinLiLin]

Thank you for the question. For the density plot, CMplot draws colored segment for each marker rather than each bin, for example, if we set the window size to be the length of one chromosome, in which there is only one marker at the middle, then CMplot will draw a green segment at the middle, instead of painting the entire chromosome in green.

[ELPSYCONGRO977]

I understand now, thank you for your explanation！

Thank you for the question. For the density plot, CMplot draws colored segment for each marker rather than each bin, for example, if we set the window size to be the length of one chromosome, in which there is only one marker at the middle, then CMplot will draw a green segment at the middle, instead of painting the entire chromosome in green.