User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek500
Reputation:
500
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Trusted
Location:
Switzerland
Last seen:
6 days, 20 hours ago
Joined:
5 years ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 64 results • page 2 of 7 • next >
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... Partially, the itemRgb column contains color definitions but they are not recognised as such by Gviz. In Gviz this columns simply represent grouping (features) and you need to define color for every group (feature). Hope that helps. Robert > On 6 Dec 2017, at 13:58, ta_awwad [bioc] <noreply@b ...
written 4 months ago by Robert Ivanek500
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... You need to provide the specific colours as additional arguments to plotTracks function or to AnnotationTrack.   plotTracks(hmmTrack, "#FF0000"="#FF0000", "#FFFF00"="#FFFF00", "#FF4500"="#FF4500") ...
written 4 months ago by Robert Ivanek500
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Answer: A: Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... I fixed that in Bioc version 3.6 and 3.7. The new version of Gviz in both bioc branches should be available in next days.  Thanks for reporting it. Robert   ...
written 4 months ago by Robert Ivanek500
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Answer: A: Normalization of AlignmentsTrack / coverage plot by library size
... Hi, You did not provide any code. It is hard to guess where the problem could be.  Typical mistake is not using full argument name. You need to provide the transformation function as argument called "transformation". The name has to be exact. For example this works for me: library(Gviz) afrom &l ...
written 5 months ago by Robert Ivanek500
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Answer: A: Gviz ChromHMM colouring for AnnotationTracks
... Hi, I can produce a colored plot  annotationTrack above: Tcell_effmem_pblood <- data.frame(seqnames = c("chr3", "chr3", "chr3", "chr3", "chr3"), start = c(3151401L, 3152201L, 3167601L, 3168001L, 3168401L), end = c(3152200L, 3152600L, 3168000L, 3168400L, 3169400L), ...
written 5 months ago by Robert Ivanek500
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Answer: A: Cannot specify groups when overlaying aligned read tracks
... Hi John, You can either use annotation tracks and then code similar to this one should work: T1 <- AnnotationTrack(reads1, feature = factor(rep("sample 1",length(reads1)), levels = c("sample 1", "sample 2")), shape = "box", showId=FALSE) T2 <- AnnotationTrack(reads2, feature = factor(rep("sa ...
written 5 months ago by Robert Ivanek500
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... You need to set ucscChromosomeNames to FALSE. BTW. what is the meaning of "!!!!???" is this a command? options(ucscChromosomeNames=FALSE) ...
written 5 months ago by Robert Ivanek500
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... Have you also switched off UCSC chromosome naming convention? options(ucscChromosomeNames=FALSE) Otherwise it is for me hard to help without seeing the data and complete code. Can you share it? ...
written 5 months ago by Robert Ivanek500
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Comment: C: Givz Doesn't plot coverage genetracks that are aligned against ensemble ref
... You can either use gene model based on ensembl or simply replace the seqlevels in your  ensGenes. seqlevels(ranges(ensGenes)) <- sub("^chr", "", seqlevels(ranges(ensGenes)))   ...
written 5 months ago by Robert Ivanek500
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Comment: C: Gviz sashimi read count
... To get those numbers via Gviz seems to me too complicated. You can use package GenomicAlignments to get those numbers from BAM files directly: function readGAlignments or readGAlignmentPairs to read in the data from BAM file and summarizeJunctions to produce the counts for junctions. ...
written 11 months ago by Robert Ivanek500

Latest awards to Robert Ivanek

Scholar 24 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 24 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 2.1 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.3 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.6 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.0 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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