Need Help With Circos
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Entering edit mode
9.2 years ago
bibb77 ▴ 90

Hi everyone, I'm making a nice circo plot for my research and I'm having a trouble trying to plot axes for several stacked data tracks, so I need to place the axes on front with the Z = 10 coordinate. In the documentation for Axes and background http://circos.ca/documentation/tutorials/quick_start/axes_and_backgrounds/lesson, is pointed out an option to draw axes inside a bare plot block <plot> not indicating a specific type of plot, just a bare plot block. The problem is when I run the .conf file, the prompt says that I need to specify the type of plot to be draw... weird thing since the documentation says the opposite...

This is my code:

<plot>
r0        = 0.83r
r1        = 0.98r
z = 10
<axes>
<axis>
position = 0.5r
color     = grey
thickness = 2
</axis>
<axis>
position = 0.166666r
color     = grey
thickness = 2
</axis>
<axis>
position = 0.833333r
color     = grey
thickness = 2
</axis>
</axes>
<backgrounds>
<background>
color = vvlgrey
</background>
</backgrounds>
</plot>

The error is:

 *** CIRCOS ERROR ***

  You must specify a type for a track. Choose one of
  [scatter,line,histogram,heatmap,highlight,tile,text,connector].

Hope you can help me, if you need more information just ask and I'll be glad to provide it

• 2.9k views
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Hi, could you state the biological relevance of your visualization?

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0
Entering edit mode

Yes!, the track I want to display is about SNV densities in 100kb windows across the genome. In the axes block (not able to plot yet) I want to show lines for standard deviations, the axis plotted in the position 0.5r is showing SD = 0, so the window are near to the mean number of variants; the line plotted at 0.16666r shows SD = -2 so lower densities, and line at 0.8333r shows SD = 2 so genomic windows very rich in variants. All this will help to pinpoint interesting high-low genomic regions for further examination (genes affected with those variants, etc).

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