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Automatic chaining (requested by @malonge, he suggested that its a simple algorithm)
Applicable to synteny views as well, and probably will want to share code in the long run.
gbrowse_syn curren…
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Hi there,
I created a dotplot with pafR to compare large genomes,
altough I can't really read the dotplot since the lines of the figure (the raster) makes it hard
to see where the genomes are sim…
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While following through the readthedocs tutorial, I have some confusion about the dotplot function.
`ns.pl.dotplot(adata, markers_dict, cluster_header, dendrogram = dendrogram, save = True, output_f…
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- [ x] Additional function parameters / changed functionality / changed defaults?
- [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?
- [ x] New plot…
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In version 1.6.5:
- [ ] Added [spectra](https://github.com/dpeerlab/spectra) to calculate the score of geneset
- [ ] Added [Starfysh](https://www.nature.com/articles/s41587-024-02173-8#Abs1) to inte…
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Hi, I am trying to identify the syntenic pattern. I have three genomes to compare one is diploid A (2x), B- hexaploid(6x) and C- allododecaploid (12x). The results I am getting A-B (1:4) instead of 1…
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Dear Author,
I encountered an issue while creating dot plots and heatmaps using your example data burkhardt21. I am using the module matrix information located in adata.obsm['X_gem'], but the resul…
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This is an enhancement request: Could you parallelize the construction of dotplots (and add a `--threads` argument)?
We really appreciate the work that you have done on `trycycler` (and `unicycler`…
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Hi there,
I currently have a dotplot generated with CanvasXpress showing this:
The current datset inputte…
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I would like to change the var name when plotting dotplot by setting the `gene_symbols` to the desired name. But this generates the NameError. Below is an example using the scanpy built-in dataset.
…