Question: ggbio circular plot y axis scale
0
gravatar for Miss Agnieszka Aleksandra Golicz
4.1 years ago by
Australia

Hello,

I am using ggbio to plot snp frequencies.

I have a following GRanges object (named lost):

GRanges object with 6 ranges and 2 metadata columns:
      seqnames             ranges strand |            id       freq
         <Rle>          <IRanges>  <Rle> |   <character>  <numeric>
  [1]        1 [      1,       1]      * |        ID_1.0 0.04444444
  [2]        1 [ 437649,  437649]      * |  ID_437649.87 0.08000000
  [3]        1 [ 875298,  875298]      * |  ID_875298.74 0.09333333
  [4]        1 [1312947, 1312947]      * | ID_1312947.61 0.01369863
  [5]        1 [1750596, 1750596]      * | ID_1750596.48 0.03703704
  [6]        1 [2188245, 2188245]      * | ID_2188245.35 0.05194805
  -------
  seqinfo: 9 sequences from an unspecified genome

And use code below to make a circular plot:

p <- ggbio()

p <- p + circle(lost, geom = "line", color = "steelblue", aes(y=freq), grid=TRUE, ylim=c(0,max(tMS$freq)))

p <- p + circle(chrs, geom = "ideo", fill = "gray70")

p <- p + circle(chrs, geom = "scale", size = 2)

p <- p + circle(chrs, geom = "text", aes(label = seqnames), vjust = -0.5, size = 3)

And end up with a nice plot ( http://jmp.sh/X89VERH ). However, I would like to add min and max y values to the plot (label grids?)

Agnieszka

 

 

 

ggbio • 1.2k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Miss Agnieszka Aleksandra Golicz40
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