Question: Circos plot for ecoli genome
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gravatar for raya.girish
2.5 years ago by
raya.girish20
raya.girish20 wrote:

Hello all I am given task for plotting circos plot I want a circular plot having 1 St circle of ecoli genome 2nd circle of upregulated genes 3 Rd circle of down regulated genes and 4th circle of GC content 2circle inside 1 3 inside 2 4inside 3 I tried using omiccircos and tutorials also I am not able to understand It would be very appreciable if some help me out. Thanks

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by raya.girish20

Your first circle should be made in the form of cytobands which form arcs of the circle.And then you can have mappings of genes (with positions)based on those cytobands. If you want to link those genes,there should be a separate data table for that. For each of arcs,mappings and links there should be a different data table.

ADD REPLYlink written 2.5 years ago by Ron950

hi Ron this i understood in omiccircos there is some commands like what is the meaning of this what this commands actually does seg.num < -10; ind.num <- 20; seg.po <- c (20:50) ;

sim.out <- sim.circos ( seg=seg.num , po=seg.po , ind=ind.num )

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by raya.girish20

You should probably look at the manual here where everything is explained: https://www.bioconductor.org/packages/devel/bioc/vignettes/OmicCircos/inst/doc/OmicCircos_vignette.pdf

"In the following example, there are 10 segments, 10 individuals, 10 links, and 10 link polygons." Basically they are defining segments and providing them values and converting those values into angles for drawing a circle.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Ron950
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