Entering edit mode
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