Entering edit mode
7.0 years ago
User000
▴
690
I am trying to plot small genes as tiles on circos plot colored red and green. The color is the 4th column in genes.tab file. But they all are grey on my circos plot I guess because of the stroke thickness and genes being small? Can anybody suggest why is that and how to improve it?
<plots>
<plot>
type = tile
file = data/genes.tab
pattern = solid
r0 = 0.94r
r1 = 0.99r
orientation = out
layers = 1
margin = 0.02u
thickness = 50
padding = 8
layers_overflow = collapse
layers_overflow_color = yellow
stroke_thickness = 3
stroke_color = vvlgrey
</plot>
What happens if you comment out the stroke options? It could well be that the stroke is too thick. Also, I don't see any green/red in your code.
green/red is my genes.tab file as the last column (color=red, color=green). I guess if I comment out my stroke_thickness option, the tiles are so small that they get invisible, but I can of cos give it a try... UPDATE: they are grey anyway, seems the default color for stroke thickness is grey. May be I can reduce the thickness of tiles, not strokes...
What if you leave out the stroke_color=vvlgrey?
I commented out both stroke thickness and stroke color..the same picture..UPDATE: The only solution I found so far is to create 2 separate files and give two different stroke colors..