Y-axis scaling

[callumjethomas]

Hi, I just had a question regarding how the Y-axis bounds are calculated when outputting to a static plot?

I've noticed that for some samples it seems like the maximum value for coverage may be cutting off points from the upper part of the graph.

Example output:

Command:

tinycov covplot -p 2 -w scaffold_6,scaffold_7 ROS3977_hap1_coverage.bam -o ROS3977_hap1_coverage.bam.plot.svg

Version:

tinycov, version 0.4.0

[cmdoret]

Hi @callumjethomas,

The upper bound of the y axis is set to 110% of the maximum coverage value:

tinycov/tinycov/tinycov.py

Line 171 in 156af47

plt.gca().set_ylim([min_count, 1.1 * max_count])

This maximum coverage value is set to max_depth:

tinycov/tinycov/tinycov.py

Line 100 in 156af47

max_count=max_depth

And max_depth is the value that is provided on the CLI option --max-depth. It defaults to 100k:

tinycov/tinycov/__main__.py

Lines 59 to 61 in 156af47

	"--max-depth",
	"-m",
	default=100000,

So basically you can just increase the value of this option on the command line:

tinycov covplot -m 200000 -p 2 -w scaffold_6,scaffold_7 ROS3977_hap1_coverage.bam -o ROS3977_hap1_coverage.bam.plot.svg