Many samples in windows

You have a value for many samples in windows along a genome: the depth of each sample, a copy number, a methylation level.

karyon NC_000962.3 --heatmap depths.tsv --relative \
  --with-tree tree.nwk --label depth -o samples.svg

One row per sample and one cell per window, in the order of the tree's tips. --relative reads each sample against its own median, so 1× is its usual depth, drawn pale: a sample sequenced deeper is not a darker row, and what changed along the genome is what stands out, a loss in blue and a gain in pink. Here one clade lost a stretch, and three samples carry another twice. A table of windows does not say how long the sequence is, so karyon draws as far as its last window and says so; write the span, as NC_000962.3:1-4,411,532, to set it yourself.

Your table

As bedtools unionbedg writes it: a sequence, a start and an end, counted from 0 as BED is, then one column per sample, named in the header.

bedtools unionbedg -header -names S01 S02 S03 -i S01.bg S02.bg S03.bg > depths.tsv

deepTools' multiBigwigSummary --outRawCounts writes the same shape, and is read too, as is the long form, a sequence, a start, an end, a sample and its value to a row.

Change it

To	Write
The values as they are	leave out --relative
Log ratios, read either side of nought	--center 0 in place of --relative
What is known about each sample, beside the rows	--traits samples.tsv
Thinner rows	--row-height 6
One stretch of the genome	NC_000962.3:1,300,000-1,600,000 as the place

The example file: depths.tsv, with tree.nwk. Every option: karyon help heatmap, or the command line reference.