User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek430
Reputation:
430
Status:
Trusted
Location:
Switzerland
Last seen:
5 days, 13 hours ago
Joined:
4 years, 9 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 57 results • page 1 of 6 • next >
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Answer: A: Combine multiple sashimis stretching over the same intron
... It is not a bug. I guess, that the reads do not start at exactly same position. You can use argument sashimiFilterTolerance and set it to small integer (5L) to merge those into one arc. It is describe in the vignette. Best Robert ...
written 26 days ago by Robert Ivanek430
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Answer: A: Gviz GenomeAxisTrack Annotation
... Dear Russ, Thanks for reporting the bug, it is fixed in 1.23.2 (devel) 1.22.2 (release). Should be available in next few days. Best Robert   ...
written 5 weeks ago by Robert Ivanek430
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Comment: C: Gviz ChromHMM colouring for AnnotationTracks
... I hope I understood you correctly.  By setting argument col you can change the border color of all track items. see Gviz vignette, chapter AnnotationTrack.  So by setting it to  col="transparent" you can get rid of the lines: Tcell_effmem_pblood <- data.frame(seqnames = c("chr3", "chr3", "chr3 ...
written 5 weeks ago by Robert Ivanek430
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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 6 weeks ago by Robert Ivanek430
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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 6 weeks ago by Robert Ivanek430
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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 6 weeks ago by Robert Ivanek430
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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 8 weeks ago by Robert Ivanek430
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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 9 weeks ago by Robert Ivanek430
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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 9 weeks ago by Robert Ivanek430
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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 12 weeks ago by Robert Ivanek430

Latest awards to Robert Ivanek

Scholar 21 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 21 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 21 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 23 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 23 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.0 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 2.8 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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