Question: I am wondering whether Gviz can support a plot like ggridges
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gravatar for shangguandong1996
25 days ago by
shangguandong19960 wrote:

Hi Dr.Ivanek. I am wondering whether Gviz can support plot like ggridges. For someone like me want to plot several samples like IGV, it will be very helpful. I have tried to ues OverlayTrack, but I think plot like ggridges(joy plot) may also be a good choice.

Best wishes. Guandong Shang

gviz • 91 views
ADD COMMENTlink written 25 days ago by shangguandong19960

Hi Guandong,

And the current implementation of DataTrack (type horizon) would not be sufficient?

Best Robert

ADD REPLYlink written 25 days ago by Robert Ivanek660

Thanks for your Nice Reply ! I indeed found the horizon, but for this type. I have two problem.

  • Actually, I dont know how to get the data like twoGroups from several bw file. Please forgive my immature GRanges operation :)

just like

```{r} a <- import("1.bw")

b <- import("2.bw")

head(a) GRanges object with 6 ranges and 1 metadata column: seqnames ranges strand | score <rle> <iranges> <rle> | <numeric> [1] Chr1 1-70 * | 0 [2] Chr1 71-90 * | 0.0645798966288567 [3] Chr1 91-200 * | 0.12916000187397 [4] Chr1 201-250 * | 0.25832000374794 [5] Chr1 251-360 * | 0.193739995360374 [6] Chr1 361-440 * | 0.0645798966288567


seqinfo: 7 sequences from an unspecified genome

head(b) GRanges object with 6 ranges and 1 metadata column: seqnames ranges strand | score <rle> <iranges> <rle> | <numeric> [1] Chr1 1-10 * | 0.083200603723526 [2] Chr1 11-30 * | 0.124801002442837 [3] Chr1 31-50 * | 0.166400998830795 [4] Chr1 51-60 * | 0.208002001047134 [5] Chr1 61-70 * | 0.291202008724213 [6] Chr1 71-80 * | 0.332803010940552


seqinfo: 7 sequences from an unspecified genome ```

  • And Second problem is if my several group(maybe 5-7 groups) bamCoverge in some range is similar。The horizon plot will looks weird.

Guandong Shang

ADD REPLYlink modified 25 days ago • written 25 days ago by shangguandong19960
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