Question

I am wondering whether Gviz can support a plot like ggridges

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Guandong Shang ▴ 40

@shangguandong1996-21805

Last seen 2.2 years ago

China

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 • 1.1k views

ADD COMMENT • link 5.1 years ago Guandong Shang ▴ 40

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Hi Guandong,

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

Best Robert

ADD REPLY • link 5.1 years ago Robert Ivanek ▴ 750

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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 REPLY • link 5.1 years ago Guandong Shang ▴ 40