Issue #13: FACS file parsing breaking

[robertaboukhalil]

This PR is to address issue #13.

Initially, it seemed like the issue was that, given a FACS file, Ginkgo could only pick a CN multiplier within [1.5, 6], even though a cell was marked as e.g. ploidy 1.3. However, looking more closely at the code, the multiplier is correctly set by the FACS file regardless of its value.

So Ginkgo's CN calculation works fine; where it breaks is when it tries to plot the SoS error plot; this is where it assumes the CN multiplier is within [1.5, 6], so this PR updates that SoS plot such that it shows:

• which ploidy Ginkgo would have guessed if no FACS file was provided
• which ploidy was chosen from the FACS file (even if outside [1.5, 6])
• the SoS error for that FACS ploidy

cc: @jpritt: I sent you an invite to become a collaborator on this repo so that I can add you as a reviewer

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Sample output (with FACS file):

• http://robertaboukhalil.com/data/ginkgo/issue13/facs/hg19.T1_SoS.jpeg
• http://robertaboukhalil.com/data/ginkgo/issue13/facs/hg19.T2_SoS.jpeg
• http://robertaboukhalil.com/data/ginkgo/issue13/facs/hg19.T3_SoS.jpeg

Sample output (without FACS file):

• http://robertaboukhalil.com/data/ginkgo/issue13/nofacs/hg19.T1_SoS.jpeg
• http://robertaboukhalil.com/data/ginkgo/issue13/nofacs/hg19.T2_SoS.jpeg
• http://robertaboukhalil.com/data/ginkgo/issue13/nofacs/hg19.T3_SoS.jpeg

(hg19.T1 is the cell that currently fails in Ginkgo)

[mschatz]

Looks great. Thanks for working on this!

Mike

[robertaboukhalil]

Thanks Mike! Is this deployed to qb.cshl.edu?

[andrewrlynch]

Hi all,
Thank you all for being so responsive and working on this. I've tried running these files again with the FACS file and have been getting the same errors I described earlier. Have these changes been deployed?

Thanks again,
Andrew