Gviz error after updating R
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Entering edit mode
ta_awwad ▴ 10
@ta_awwad-11382
Last seen 5 months ago
Frankfurt am Main

 

Hi everybody, I have actually weird situation. my Gviz script was working perfectly but after I updated my R version I am getting the following error message after running plotTracks:     

Error in (function (classes, fdef, mtable)  :
      unable to find an inherited method for function 'displayPars<-' for signature '"character", "list"'

here is my code:

from <- 12345500
to <- 12345678
chr <- 'chr3R'
gen <- 'dm3' 

refGenes <- UcscTrack(genome=gen, chromosome= chr,
                           track="RefSeq Genes", from=from, to=to,
                           trackType="GeneRegionTrack", rstarts="exonStarts",
                           rends="exonEnds", gene="name", symbol="name2",
                           transcript="name", strand="strand", fill="#048edd",
                           stacking="squish", name="RefSeq", col="#000000",
                           col.line= "#000000", fontcolor.group="#000000",
                           min.height= 4, col.sampleNames="black",
                           background.title="white",col.axis="black",
                           col.title="black")

A <- DataTrack(range = cpwg,
                 genome = gen,
                 chromosome = chr,
                 type = "h",
                 col="#ff0000",
                 ylim=c(0, 300), name="CP190", col.sampleNames="black",
                 background.title="white",col.axis="black",
                 col.title="black")

B <- DataTrack(range = gcwg,
                   genome = gen,
                   chromosome = chr,
                   type = "h",
                   col="#0000ff",
                   ylim=c(0, 200), name="Gcn5", col.sampleNames="black",
                   background.title="white",col.axis="black",
                   col.title="black")

C <- DataTrack(range = ctwg,
                  genome = gen,
                  chromosome = chr,
                  type = "h",
                  col="#008000",
                  ylim=c(0, 300), name="CTCF", col.sampleNames="black",
                  background.title="white",col.axis="black",
                  col.title="black")

D <- DataTrack(range = bewg,
                  genome = gen,
                  chromosome = chr,
                  type = "h",
                  col="#a60ab0",
                  ylim=c(0, 300), name="BEAF-32", col.sampleNames="black",
                  background.title="white",col.axis="black",
                  col.title="black")

E <- DataTrack(range = suwg,
                  genome = gen,
                  chromosome = chr,
                  type = "h",
                  col="#a52a2a",
                  ylim=c(0, 300), name="Su(Hw)", col.sampleNames="black",
                  background.title="white",col.axis="black",
                  col.title="black")

axTrack <- GenomeAxisTrack(col="#000000", fontcolor="#000000")

idxTrack <- IdeogramTrack(genome= gen, chromosome=chr,
                          fontcolor= "#000000", outline=TRUE)

plotTracks(list(idxTrack, axTrack , A, B, C, D, E, refGenes),
                from=from, to=to, showTitle=T,showId=T, scale=0.1)

does anyone have an experience with such error?

Tamer

software error Gviz chipseq rnaseq • 1.1k views
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0
Entering edit mode
ta_awwad ▴ 10
@ta_awwad-11382
Last seen 5 months ago
Frankfurt am Main

thanks guys .. was my mistake .. i figured it out 

 

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