Comments (3)
Option to draw brush with the initial position such as brush: "chr:start-stop"
This is implemented in the new v0.15.0 release. See Brush for an example.
from ideogram.
@6br, thanks for these feature requests. I'll give your proposals a closer look once I'm done expanding support for cytobands (#83), likely within a few weeks.
In the meantime, if you could describe use cases for these potential enhancements, that would help me prioritize my work. I also accept pull requests!
from ideogram.
@eweitz, thanks for your reply!
My use cases are following.
- To select genomic variations in human:
In this case, annotations mean genes, SNPs or SVs, which is shown on each track. Here, I have already selected some chromosomes by annotations of genes such as related to cancer or metabolic pathway.
-
The karyotypes of selected chromosomes are shown and they should be aligned in the order of chosen because the order is related to the priority of genomic locus to select, I think.
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If I set the genomic coordinate in advance, the brush should have been moved there. The
selectedRegion
of brush should be consistent with the given coordinate in advance.
I am trying to do so (master...6br:master), but it does not seem to work well since it does not preserve the exact genomic coordinates.
-
By selecting one region from multiple chromosomes with a brush, I can narrow down the SNPs and SVs that exist in the region selected. I will use
ideogram.selectedRegion
to narrow down the external SNPs table. -
Moreover, when I click the annotation of SNPs or SVs, details of these variants will be shown. Since I want to fetch what is clicked, it requires callbacks on annotations.
I think from 1 to 3 is the important part because it seems to be tightly coupled with library's implementation.
I would be pleased if it could help your work.
Regards,
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Related Issues (20)
- API annotations not working on genomes with non "1,2,3" labelled chromosomes HOT 1
- Is there a limit to the number of keys in the legend? HOT 2
- Issue with custom organism bandfiles
- Display annotation track from a BED file HOT 8
- Support T2T human genome HOT 2
- Support gzipped BED files HOT 1
- Support for structural rearrangements HOT 4
- Histogram support for bedgraph format HOT 2
- 404 (Not Found) HOT 1
- Karyotype file of dual comparison error HOT 3
- Jupyter Notebook example no longer works HOT 5
- Chromosome disappears after being clicked for some organisms HOT 3
- Is there a way to zoom in or out ideograms to check overlapped annotations? HOT 2
- rangeSet does not support sex chromosomes HOT 4
- where is detailed documentation/wiki? HOT 1
- Two annotations layouts combined: overlaid + histogram HOT 2
- Annoatation with multiple tracks HOT 1
- Histogram with tooltip? HOT 2
- Missing regions in fly ideogram? HOT 4
- Help with Uploading a Bed file instead of a URL link HOT 6
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