User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek610
Reputation:
610
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Trusted
Location:
Switzerland
Last seen:
1 month ago
Joined:
6 years, 3 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 89 results • page 2 of 9 • next >
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Answer: A: Gviz color alignments by read strand
... The way how Gviz handles colouring for AlignmentsTrack is a bit special. It recycles colours specified in the fill.reads along the length of unique read ids (uid column). On top of it, if you plot reads as arrows, it also sorts the reads before plotting according to the strand. Maybe this piece of ...
written 6 months ago by Robert Ivanek610
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Comment: C: Gviz color alignments by read strand
... Hi Chris, what exactly do you want to achieve? Do you want to plot individual reads (coloured by the read strand) or coverage (histogram) for both strands separately? Robert ...
written 6 months ago by Robert Ivanek610
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Comment: C: Gviz: decreasing tick resolution
... Yes, that is correct. I think that installing devel version of R and all the packages might be an overkill, especially for one figure. If you do not mind to use a dirty hack you can also install the devel version of Gviz in current release version of R (assuming all dependencies for release version ...
written 6 months ago by Robert Ivanek610
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Answer: A: Gviz: decreasing tick resolution
... Hi Will, I added new parameter called ticksAt for GenomeAxisTrack. It will be available in developmental version of Gviz (1.27.5) (Bioc 3.9) Best Robert ...
written 6 months ago by Robert Ivanek610
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Comment: C: Error in `rownames : Gviz plotTracks
... I have just checked your sessionInfo and realised that you have a picture of packages from current release and some older ones, for example: GenomicRanges, GenomicFeatures, Biobase and few others. Can you please update your packages and try again?  Best Robert ...
written 6 months ago by Robert Ivanek610
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Answer: A: Gviz: Setting Up Colour / Fill for AnnotationTrack (strand-dependent colour)
... Hi, You can colour the individual items in the AnnotationTrack by setting the feature to "plus" and "minus" strand. Then in plotTracks function provide two additional arguments which set colours to "plus" and "minus" features: library(Gviz) data(collapseTrack) strand(ctrack) <- rep(c("+","-", ...
written 6 months ago by Robert Ivanek610
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Comment: C: Error in `rownames : Gviz plotTracks
... Hi, I have just checked the code in both release and level versions and it worked for me. Could you please your sessionInfo?  Best, Robert   ...
written 6 months ago by Robert Ivanek610
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Answer: A: Gviz single side margin for plotTracks
... I updated the code in both versions (release, devel) that it can take four different values for margin definition (similar to par). If you provide only two, it will use them as before. It will be available in next versions. ...
written 7 months ago by Robert Ivanek610
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Comment: C: Gviz single side margin for plotTracks
... Hi Alex, I can update the code to take all four values c(bottom, left, top, right) into account but it will not be compatible with current specification of the margin c(width, height). Therefore I can only push this change into devel version of Gviz (Bioc 3.9). Best Robert ...
written 7 months ago by Robert Ivanek610
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Comment: C: Gviz single side margin for plotTracks
... Dear Alex, Can you provide a reproducible example? The Gviz is using grid graphics so par cannot work. Best Robert ...
written 7 months ago by Robert Ivanek610

Latest awards to Robert Ivanek

Popular Question 6 months ago, created a question with more than 1,000 views. For IdeogramTrack and bigWig file errors in Gviz
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 6 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 6 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 2.2 years 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: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
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 3.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.2 years ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 3.3 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.4 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.4 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.5 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.8 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 4.3 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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