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User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek590
Reputation:
590
Status:
Trusted
Location:
Switzerland
Last seen:
9 hours ago
Joined:
5 years, 10 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 82 results • page 1 of 9 • next >
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Answer: A: Truncated Gviz plot
... Hi Mario, Thanks for reporting it. I changed settings for "sashimi" plots in Gviz. There should be new version compiled in release (1.26.5) and in development (1.27.6). They should be available in next few days. Let me know if that fixed your problem. Best Robert ...
written 1 day ago by Robert Ivanek590
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Comment: C: Error loading Gviz package object path is not exported by namespace:Rsamtools
... Hi, what is the version of `Gviz` package you are using? Best Robert ...
written 5 weeks ago by Robert Ivanek590
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Comment: C: Gviz: decreasing tick resolution
... You need to specify the positions of tick marks, i.e. seq(280e3, 320e3, 40e3). Complete example: library(Gviz) axisTrack <- GenomeAxisTrack() plotTracks(axisTrack, from=270e3, to=330e3) with ticksAt parameter: plotTracks(axisTrack, from=270e3, to=330e3, ticksAt=seq(280e3, 320e3, 40e3)) ...
written 6 weeks ago by Robert Ivanek590
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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 7 weeks ago by Robert Ivanek590
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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 7 weeks ago by Robert Ivanek590
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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 7 weeks ago by Robert Ivanek590
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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 7 weeks ago by Robert Ivanek590
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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 8 weeks ago by Robert Ivanek590
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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 8 weeks ago by Robert Ivanek590
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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 8 weeks ago by Robert Ivanek590

Latest awards to Robert Ivanek

Scholar 6 weeks ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 6 weeks ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 22 months ago, created an answer that has been accepted. For A: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
Scholar 22 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 22 months ago, created an answer that has been accepted. For A: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
Scholar 22 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 2.8 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 GeneRegionTrack draw only one gene in the range
Scholar 2.9 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"
Scholar 3.0 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.1 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 3.9 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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