User: Robert Ivanek

gravatar for Robert Ivanek
Robert Ivanek660
Reputation:
660
Status:
Trusted
Location:
Switzerland
Last seen:
2 weeks, 5 days ago
Joined:
6 years, 8 months ago
Email:
r************@unibas.ch

Posts by Robert Ivanek

<prev • 104 results • page 1 of 11 • next >
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Comment: C: Gviz change color of groups
... Hi Kristian, You can achieve it with defining group as a `factor`. Best Robert ``` library(Gviz) set.seed(123) gr <- GRanges("chr1", IRanges(sort(sample(999, 100)), width=1)) mcols(gr) <- matrix(runif(400), ncol=4) dtTrack1 <- DataTrack(range=gr, genome="mm9", name="random data", group ...
written 19 days ago by Robert Ivanek660
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Comment: C: I am wondering whether Gviz can support a plot like ggridges
... Hi Guandong, And the current implementation of [`DataTrack`](https://master.bioconductor.org/packages/3.10/bioc/vignettes/Gviz/inst/doc/Gviz.html#43_datatrack) (type `horizon`) would not be sufficient? Best Robert ...
written 27 days ago by Robert Ivanek660
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Answer: A: Gviz UCSC tracks not visible
... Hi, There were several issues in your code, you need to pay attention to extract correct information from UCSC tables. You also did not provide code which works. There were some parts missing and few typos. Here is the code which works for me. Best Robert ``` library(rtracklayer) library(Gviz) l ...
written 7 weeks ago by Robert Ivanek660
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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 12 weeks ago by Robert Ivanek660
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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 12 weeks ago by Robert Ivanek660
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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 12 weeks ago by Robert Ivanek660
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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 3 months ago by Robert Ivanek660
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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 3 months ago by Robert Ivanek660
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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 3 months ago by Robert Ivanek660
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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 3 months ago by Robert Ivanek660

Latest awards to Robert Ivanek

Scholar 4 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Popular Question 11 months ago, created a question with more than 1,000 views. For IdeogramTrack and bigWig file errors in Gviz
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 11 months ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 11 months ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz: AlignmentsTrack from a bam file with non-UCSC chromosome names
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Gvis: Adding colour and transparency to overlaid alignment tracks
Scholar 2.6 years ago, created an answer that has been accepted. For A: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
Scholar 2.6 years ago, created an answer that has been accepted. For A: Gviz GeneRegionTrack draw only one gene in the range
Scholar 2.6 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 GeneRegionTrack draw only one gene in the range
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 3.8 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 3.9 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 4.2 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
Scholar 4.7 years ago, created an answer that has been accepted. For A: gviz: error when plotting BiomartGeneRegionTrack with just.group="above"

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