Question

Gradient dotplot

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sophieagger • 0

@78ca6878

Last seen 3.1 years ago

Denmark

I've been playing around with GViz, but I cannot for the life of me figure out how to make my plot. I would like to make my datatrack a dotplot, colored by a gradient based on a different variable. Basically:

ggplot(fst_snpchr10_51556910,aes(x=POS,y=Z_FST))+geom_point(aes(color=R2),  size=1)

I just can't figure out how to do that with GViz and I would really like to have the annotationtrack.

Thanks!

Gviz • 1.5k views

ADD COMMENT • link 3.2 years ago sophieagger • 0

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It is not possible to color the points in a DataTrack based on a continuous variable at the moment.

ADD REPLY • link 3.2 years ago Robert Ivanek ▴ 750

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But this a bit "hackish" solution might work for you. It takes advantage of groups which are defined as separate columns.

library(RColorBrewer)
library(Gviz)

set.seed(100)
gr <- GRanges("chr1", IRanges(seq(1,5000,5), width=1), strand="+",
              val=rnorm(1000, 0, 5))
# cut values according to breaks
rr <- c(-20, seq(-12,12,length.out=9), 20)
gr$fac <- cut(gr$val, breaks=rr, include.lowest=TRUE)

# build new mcols with columns representing groups
temp <- vapply(levels(gr$fac), function(lev, val=gr$val, fac=gr$fac) {
    ifelse(fac==lev, val, NA)}, FUN.VALUE=numeric(length(gr))) 
mcols(gr) <- temp

# grouping (order of levels is important) and plot
grps <- factor(colnames(mcols(gr)), levels=colnames(mcols(gr)))
plotTracks(DataTrack(gr), col=rev(brewer.pal(11, "RdBu")[-6]), groups=grps)

ADD REPLY • link 3.2 years ago Robert Ivanek ▴ 750

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That's smart, I'm a bit worried that it'll break my computer if I get enough levels in there to make me happy, but I'll give it a try.

ADD REPLY • link 3.2 years ago sophieagger • 0