Bernat Gel
Bernat Gel
clipping does not take into account the R0 and r1 values. Modify processClipping to take them into account
Add an addtional parameter to plotKaryotype called "seqlevelsStyle". If not NULL, change the seqlevelsStyle of the genome and the cytobands before plotting the genome. This would solve many of the...
Currently the clipping option works only when zoom is active. Removing this limitation could be beneficial in many situations, even at the cost of a small performance degradation.
Read the chromosome lengths from a fa.fai (fasta index) file. Should decide if include the functionality on toGRanges or in karyoploteR. Note: use `scanFaIndex` from Rsamtools
It would be useful to be able to autoload a genome given its GenBank accession number or genebank file. It could work via implementing a GeneBank parsing feature to toGRanges?
Add the option to give a normalization factor to plot coverage values from BAMs and BigWigs. With that it would be possible, for example, to use the normalization factor computed...
If r1 is NULL and r0 has two elements, r0 and r1, use them as r0 and r1. This will reduce the typing when using autotrack.
Similar to the two triangles in UCSC
Adding base numbers with very small tick dist is too slow. Reimplement to take into account zoomed in region before plotting.
kpPlotBAMDensity was written with large windows and the whole genome in mind. But for smaller windows and specially for small parts of the genome it can be very innefficient. Optimize...