Circos plot for overlapping values/colors
francy....@gmail.com
Dear CIRCOS experts,
I have a file with many genes across the genome, and each with a different color depending on whether a SNP within the gene has been associated with a phenotype. I would like to create a plot using circos representing these genes across the genome with the different colors. I think the right plot to use in this case is a 'tiles' plot because there are many overlapping genes, additionally there could be different colors for the same gene if the SNPs in the same gene have been associated with more than one phenotype. I have also tried with 'highlights' and with 'heatmap' (using the phenotype colors as the factor levels) but I don't think this is the way to go because I cannot see the overlaps if I use these plots, which is what I am mostly interested in.
I am attaching the example data file. There are genes with the same color if the gene has been associated with the same phenotype more than once, and the colors are assigned based on the phenotype. I am also attaching the configuration file I am using.
However, I can't get the colors in the tiles plot to show up correctly: there are some colors that do not come up, and I have black lines while I do not have a color 'black' for any of the phenotypes. I have tried adjusting the layers, and the stroke_thickness, but these black lines remain and the correct colors sill do not show. I am attaching the plot I am getting now.
Can you please help me understand why this is happening, if you have any thoughts about what I am doing wrong? I really appreciate any suggestions!
Thank you in advance for your help!
Fra
Martin Krzywinski
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