Question

bam files to hilbert curve

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Entering edit mode

adklts • 0

@adklts-21974

Last seen 3.6 years ago

Good day. I am trying to convert on the chromosome from bam file to GRobject and the to plot with package HilbertCurve. But I receive an error

> hc = GenomicHilbertCurve(chr = "chr1", background = reads  level = 5, reference = TRUE, 
Error: unexpected symbol in "hc = GenomicHilbertCurve(chr = "chr1", background = reads  level"
>     reference_gp = gpar(lty = 1, col = "grey"), arrow = FALSE)
Error: unexpected ',' in "    reference_gp = gpar(lty = 1, col = "grey"),"
> hc_segments(hc, g, gp = gpar(lwd = 6, col = rand_color(length(g))))
Error in grid.Call.graphics(C_downviewport, name$name, strict) : 
  Viewport 'hilbert_curve_0' was not found

My code in the follow

library(chromstaR)
library(GenomicRanges)
library(HilbertCurve)
library(circlize)
bampath <-"C:/Users/Admin/Documents/R/win-library/3.6/GenomicRanges/extdata/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam"
bam <- bampath

reads <- readBamFileAsGRanges(bam, chromosomes='chr1', pairedEndReads=FALSE,
                    min.mapq=10, remove.duplicate.reads=TRUE)


hc = GenomicHilbertCurve(chr = "chr1", background = reads  level = 5, reference = TRUE, 
    reference_gp = gpar(lty = 1, col = "grey"), arrow = FALSE)
hc_segments(hc, g, gp = gpar(lwd = 6, col = rand_color(length(g))))

I appreciate very much if you help me to create a Hilbert curve from bam files or to convert bam files to the data frame and then to use in the Hilbert curve package. Thank you!

HilbertCurve error bamfiles GRobject • 1.5k views

ADD COMMENT • link 5.2 years ago adklts • 0

score 2 · Accepted Answer · 2019-09-24

2

Entering edit mode

Zuguang Gu ▴ 290

@zuguang-gu-7797

Last seen 22 days ago

Germany / Heidelberg / DKFZ

You missed a comma here:

hc = GenomicHilbertCurve(chr = "chr1", background = reads  level = 5, 
                                                        ~~~~ <---

ADD COMMENT • link 5.2 years ago Zuguang Gu ▴ 290

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Entering edit mode

Thank you very much . But now giving me new error

Error in GenomicHilbertCurve(chr = "chr1", background = reads, level = 5, : Chromosomes cannot be duplicated in background regions.

hcsegments(hc, g, gp = gpar(lwd = 6, col = randcolor(length(g)))) Error in grid.Call.graphics(Cdownviewport, name$name, strict) : Viewport 'hilbertcurve_0' was not found

ADD REPLY • link 5.2 years ago adklts • 0

1

Entering edit mode

Value for background argument should contain ranges of chromosomes. In your code, I think reads contains the mapped regions that needs to be visualized. Try:

hc = GenomicHilbertCurve(chr = "chr1", level = 5)
hc_points(hc, reads, col = "red")

ADD REPLY • link 5.2 years ago Zuguang Gu ▴ 290

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Entering edit mode

Thanks again. We pass the problem of duplicate chromosome but appear Error in .local(object, ...) : unused argument (col = "red")

ADD REPLY • link 5.2 years ago adklts • 0

1

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Sorry, it should be

hc = GenomicHilbertCurve(chr = "chr1", level = 5)
hc_points(hc, reads, gp = gpar(col = "red"))

ADD REPLY • link 5.2 years ago Zuguang Gu ▴ 290

0

Entering edit mode

Giving error

Error in grid.Call.graphics(Cdownviewport, name$name, strict) : Viewport 'hilbertcurve_1' was not found