User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek640
Reputation:
640
Status:
Trusted
Location:
Switzerland
Last seen:
4 weeks, 1 day ago
Joined:
6 years, 6 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 101 results • page 1 of 11 • next >
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Answer: A: Extracting read coverage data from a Gviz AlignmentsTrack
... Hi, You can simply read in the part of your BAM file with `GAlignments` function and afterwards extract junction counts with `summarizeJunctions`, both function come from `GenomicAlignments` package. ...
written 29 days ago by Robert Ivanek640
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Comment: C: GVIZ stacking error
... The workaround would be to use `collapse=FALSE` as a parameter for `AnnotationTrack` or `plotTracks` function. ...
written 29 days ago by Robert Ivanek640
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Comment: C: Legend color mix-up in grouped Gviz plot
... Hi, thanks for pointing that out. It should be fixed in both (release and development) versions in next few days. ...
written 4 weeks ago by Robert Ivanek640
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Answer: A: I am wondering whether Gviz can plot thin box(noncoding part) directly from GRan
... Dear Guandong Shang, You can create `TxDb` object form your GTF file by using `makeTxDbFromGFF` function from `GenomicFeatures` package. Afterwards you can make `GeneRegionTrack` and plot it with `Gviz`. Best Robert ``` library(GenomicFeatures) TxDb <- makeTxDbFromGFF("test.gtf") genemodel_tra ...
written 6 weeks ago by Robert Ivanek640
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Answer: A: How to arrange multiple Gviz plots into a multipanelfigure?
... Thanks. We are happy you like it. What about this? ``` grid.newpage() # 2x2 layout pushViewport(viewport(layout=grid.layout(2, 2))) # 1,1 first plot pushViewport(viewport(layout.pos.col=1,layout.pos.row=1)) Gviz::plotTracks(list(ideogram, genomeaxis, siteA), add=TRUE) popViewport() # 2,2 second ...
written 6 weeks ago by Robert Ivanek640
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Comment: C: GVIZ stacking error
... The reason for this behaviour is following: `Gviz` checks the resolution of the plotting device and tries to collapse features for which there might not be enough space/resolution in the resulting plot. It collapses them based on a hierarchy. Maybe it is set to strictly, I will try to relaxed it. ...
written 7 weeks ago by Robert Ivanek640
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Comment: C: GVIZ stacking error
... I cannot look into it unless you generate a reproducible example with that error (or share the GFF file) ...
written 7 weeks ago by Robert Ivanek640
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Comment: C: GVIZ stacking error
... Hi, Could you please send me your GFF file, or at least a relevant part of it? Thanks, Robert ...
written 8 weeks ago by Robert Ivanek640
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Comment: C: How to center data points on coordinates (bases) in Gviz?
... Thanks for bringing that up. There was a bug in the `Gviz` and I pushed fix into both branches (release 1.28.1 and devel 1.29.1). Now the data points, ticks and tick-marks should be aligned. Let me know if that works for you. BTW. When reading the `bedGraph` manually, keep in mind that start is "0 ...
written 8 weeks ago by Robert Ivanek640
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Comment: C: Normalized sashimi plots with Gviz
... Can you be more specific? with detailed example? ...
written 9 weeks ago by Robert Ivanek640

Latest awards to Robert Ivanek

Scholar 9 weeks ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Popular Question 9 months ago, created a question with more than 1,000 views. For IdeogramTrack and bigWig file errors in Gviz
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 9 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 9 months 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: AlignmentsTrack from a bam file with non-UCSC chromosome names
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 2.5 years ago, created an answer that has been accepted. For A: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
Scholar 2.5 years ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 2.5 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 GeneRegionTrack draw only one gene in the range
Scholar 3.5 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.6 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.7 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 3.7 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 4.0 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 4.5 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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