User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek530
Reputation:
530
Status:
Trusted
Location:
Switzerland
Last seen:
6 days, 10 hours ago
Joined:
5 years, 3 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 69 results • page 2 of 7 • next >
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Answer: A: gviz ideogramTrack connection error
... I have just try it on both release and developmental version and both works for me. In fact I used "IdeogramTrack" but I assume that was just a typo in your post. Could it be, that you are being firewall or proxy?   ...
written 5 months ago by Robert Ivanek530
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Answer: A: Gviz: Add label/title to GenomeAxisTrack
... Dear Alex, This should work, with default scheme: library(Gviz) axisTrack <- GenomeAxisTrack(showTitle=TRUE, name="chr1", background.title="lightgray", rotation.title=0) plotTracks(axisTrack, from = 1e+06, to = 9e+06) or with transparent background and tittle in dark grey: axisTrack < ...
written 5 months ago by Robert Ivanek530
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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 6 months ago by Robert Ivanek530
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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 7 months ago by Robert Ivanek530
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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 7 months ago by Robert Ivanek530
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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 7 months ago by Robert Ivanek530
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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 7 months ago by Robert Ivanek530
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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 7 months ago by Robert Ivanek530
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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 months ago by Robert Ivanek530
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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 8 months ago by Robert Ivanek530

Latest awards to Robert Ivanek

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 14 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 14 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 14 months ago, created an answer that has been accepted. For A: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
Scholar 14 months ago, created an answer that has been accepted. For A: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
Scholar 2.2 years ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
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 2.4 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.4 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.5 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"
Scholar 3.3 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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