Plotting bed8 with Sushi possible?
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maltethodberg ▴ 140
@maltethodberg-9690
Last seen 4 weeks ago
Denmark

I've been trying to use Sushi to plot a bed8-file, containing the location of a cluster and the location of the cluster "peak" in the thickStart/thickEnd columns:

library(Sushi)
bed8 <- data.frame(chrom="chr18",
                                     chromStart=100,
                                     chromEnd=125,
                                     name="ClusterX",
                                     score=0,
                                     strand="+",
                                     thickStart=110,
                                     thickStart=111)

There doesn't seem to be a custom function for this in Sushi, so I played around with plotGenes (Which can do the thin/thick plotting):

d <- data.frame(chrom=c("chr18", "chr18", "chr18"),
                                     chromStart=c(100, 110, 111),
                                     chromEnd=c(110, 111, 125),
                                     name=c("ClusterX", "ClusterX", "ClusterX"),
                                     score=0,
                                     strand=c("+", "+", "+"),
                                     type=c("utr", "exon", "utr"))

chrom <- "chr18"
chromStart <- 1
chromEnd <- 300

# Decent plot produced, but return strange output as well:
plotGenes(d, chrom=chrom, chromstart = chromStart, chromend = chromEnd, type=d$type)
[[1]]
NULL

[[2]]
function (n) 
{
    x <- ramp(seq.int(0, 1, length.out = n))
    if (ncol(x) == 4L) 
        rgb(x[, 1L], x[, 2L], x[, 3L], x[, 4L], maxColorValue = 255)
    else rgb(x[, 1L], x[, 2L], x[, 3L], maxColorValue = 255)
}
<bytecode: 0x11269a928>
<environment: 0x116c82c98>

Warning messages:
1: In Ops.factor(strand, bprange) : ‘*’ not meaningful for factors
2: In Ops.factor(strand, bprange) : ‘*’ not meaningful for factors

Is this bug or am I misspecifying something? Is there perhaps a better way of plotting bed8 files?

sushi bed • 277 views
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