search

choderalab / assaytools

Modeling and Bayesian analysis of fluorescence and absorbance assays.
http://assaytools.readthedocs.org
GNU Lesser General Public License v2.1
18 stars 11 forks source link

Improving xml2png.py #62

Open MehtapIsik opened 8 years ago

MehtapIsik commented 8 years ago

I was testing xml2png.py with Infinite results of different assay types. I will list here some suggestions:

  1. Adding usage example with type argument will be useful here: https://github.com/choderalab/assaytools/blob/master/scripts/xml2png.py#L4
  2. For single_96 type, the plots are too wide. We should adjust plot dimensions. There is empty space on x-axis for wells bigger than 12 on 96-well plot. mi_flu_hsa_lig1_20150914_172954
  3. I think adding axis labels will be great. x-axis label: Well Index, y-axis label: Fluorescence
  4. Plot title usually has None printed for 'Part of Plate' section. image https://github.com/choderalab/assaytools/blob/master/scripts/xml2png.py#L111-L124 Do we need "Part of Plate" information? Or can we assign a default "Full Plate" when xml doesn't have this information.
  5. I don't have ant 384-well data, so I couldn't test singlet_384 type but I noticed it has hard coded ligand concentration(Lstated) for plotting. Can we remove that? https://github.com/choderalab/assaytools/blob/master/scripts/xml2png.py#L404-L418
  6. The difference between types spectra and scan wasn't obvious to me.
sonyahanson commented 8 years ago

Thanks Mehtap!

bas-rustenburg commented 8 years ago

Could it also be made python 3 compatible?

bas-rustenburg commented 8 years ago

It may also be helpful if it prints the help string if called without any arguments.

jchodera commented 8 years ago

All good ideas!