Add a barplot of the summarizeFasta results

[zhuchcn]

Description

The summarizeFasta now can accept a --output-image arg and creates a barplot of the summary results. This is an example:

Any thought?

Closes #...

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
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[lydiayliu]

The example output looks fine. It worries me if "Noncoding" is also plotted cuz then you would literally only be able to see that 1 bar. Maybe it's worth adding a log10 if Noncoding is plotted (and since stacked no longer works just use one colour)?

Is the current sorting order the same as in the summarizeFasta text file?

[zhuchcn]

Log scaling sounds reasonable but it will make the stacked barplot hard to interpret, because the stacked bars are no longer proportional.

Is the current sorting order the same as in the summarizeFasta text file?

They should be in the same order

[lydiayliu]

Log scaling sounds reasonable but it will make the stacked barplot hard to interpret, because the stacked bars are no longer proportional.

Yeah so if we do log scale we can just do a single colour for the bars :) (aka not show the miscleavages)

[zhuchcn]

I added a pair of argument --plot-normal-scale/--plot-log-scale to set what scale the plot should use. If neither arg is given, it will figure out what's the best. I'm doing it by comparing the mean and median of number of peptides in each source group. So use log scale if mean is way larger than median.

This is what it looks like. Scale looks strand because it's small.

[lydiayliu]

Looking good! The only thing I can think of is whether we should exclude the entries with 0 peptides? I think it's ok eitherway (I don't think we are excluding any now)

[zhuchcn]

The only thing I can think of is whether we should exclude the entries with 0 peptides? I think it's ok eitherway (I don't think we are excluding any now)

Let's leave it in this way for now. Will be good to see some examples.