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Merge Antibody and Interface Features R scripts #1

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Merge Antibody and Interface Features R scripts #1

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jadolfbr
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@jadolfbr jadolfbr commented Jun 16, 2016 •
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This merge will get our antibody and interface R scripts into the new library structure. Some general fixes that allow Rscript to run are here as well.

  • Copy and test Antibody scripts
  • Copy and test Interface scripts
  • Fix and re-enable CDR4 option through the JSON script directly.
  • Fix ordering of sample sources generally to go with that passed in JSON file

This merge also adds the following executable scripts, some of which will be deleted after this PR is complete:

install_from_dunbrack_github.R
install_from_momeara_github.R
install_local.R
run_features.R

run_features.R takes a JSON config file and runs it.
install_local.R installs the local version, but it doesn't quite work yet.

The other two are temporary. Eventually a script like this will be part of Rosetta proper in the source/scripts/features directory.

Specific scripts that need to be fixed still

  • Interface Composition
  • Interface Hbond density
  • delta unsats

@rfalford12
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This is awesome! Going to follow your lead on this.

On Thu, Jun 16, 2016 at 7:00 PM, Jared Adolf-Bryfogle <
[email protected]> wrote:

This merge will get our antibody and interface R scripts into the new
library structure. Some general fixes that allow Rscript to run are here as
well.

  • Copy and test Antibody scripts
  • Copy and test Interface scripts
  • Fix and re-enable CDR4 option through the JSON script directly.

This merge also adds the following executable scripts, some of which will
be deleted after this PR is complete:

install_from_dunbrack_github.R
install_from_momeara_github.R
install_local.R
run_features.R

run_features.R takes a JSON config file and runs it.
install_local.R installs the local version, but it doesn't quite work yet.

The other two are temporary. Eventually a script like this will be part of

Rosetta proper in the source/scripts/features directory.

You can view, comment on, or merge this pull request online at:

#1
Commit Summary

  • initial copy of scripts. No changes yet made to them.
  • Fix all interface scripts. Remove some non-useful plots that I have
    been meaning to remove.
  • Fix all antibody scripts.
  • add script for local installation from dunbrack repo for now.
  • add a script to run the features by passing a configuration file.
  • Update README.md
  • re-implement char_as_factor in query_sample_sources.
  • Merge branch 'master' of github.com:DunbrackLab/RosettaFeatures
  • fixes.
  • fixes.
  • fixes.
  • fixes.
  • fixes.
  • fixes.
  • fixes.
  • fixes.
  • remove char_as_factor
  • comment out cdr4 option or now, until it can be set via json.

File Changes

Patch Links:

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Rebecca Faye Alford
Chemistry - Carnegie Mellon '16
Undergraduate Research Assistant - Gray Lab, Johns Hopkins

@jadolfbr
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Also, I just found a bug generally in the features reporters where the order plotted does not match the order given in the JSON file.

This is a problem for two or more sample sources, especially with the native stuck in the middle... We should fix this in this PR (and merge in the PR as it stands now soon too!)

@jadolfbr
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@momeara - any guidance on the ordering? I need it for publication, so I'm going to try to fix it now...

@momeara
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momeara commented Sep 14, 2016

What you have so far looks good, but please add .Renviron and .Rprofile to .gitignore

Keeping the sample source order consistent with the config file sounds good to me.

@jadolfbr
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Will do. I think after that, maybe we can merge in. I think the option stuff that simon is working on should be a separate PR.

@momeara
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momeara commented Sep 14, 2016

Sounds good to me!

On Wed, Sep 14, 2016 at 12:25 PM, Jared Adolf-Bryfogle <
[email protected]> wrote:

Will do. I think after that, maybe we can merge in. I think the option
stuff that simon is working on should be a separate PR.

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@jadolfbr
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Awesome - also - before I keep going - Was the ordering consistent with the JSON file before, or did I just think it was? I was pretty sure the ordering was kept, but I just wanted to make sure. I can't seem to find where the ordering is lost in compare_sample_sources

@momeara
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momeara commented Sep 14, 2016

It isn't clear to me where they are getting re-arranged, but what ever the
behavior was before, keeping them in the order in the config file seems
reasonable.

On Wed, Sep 14, 2016 at 1:08 PM, Jared Adolf-Bryfogle <
[email protected]> wrote:

Awesome - also - before I keep going - Was the ordering consistent with
the JSON file before, or did I just think it was? I was pretty sure the
ordering was kept, but I just wanted to make sure. I can't seem to find
where the ordering is lost in compare_sample_sources

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@jadolfbr
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OK. Searching for sort and order didn't show any code that could be it. Reading docs to the fromJson function, it seems that ordering of vectors should be preserved by default. Are there any other ordering functions you know of that could cause it? They are definitely sorted by sample source name in the plots.

@jadolfbr
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The configuration is sound. Order at the beginning print, order at the end during close of the dbs.

The order in query_sample_sources is messed up, however. The sources are not loaded in order - but the function isn't doing anything funky besides ddply

@jadolfbr
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I'm still not sure why this is the case. Its either underlying ddply functions or geom_indicator. I'm going to rename my variables and table this. I think maybe you could find the solution, but I'm about at my limit atm.

@jadolfbr
remove debugging info.
06299bb
@jadolfbr
make abbreviations less severe. I wish this was automatic.
50e23c0
@jadolfbr
increase length for abbreviations.
ba956a9
@jadolfbr
fix sasa plots.
0377b85
@jadolfbr
debugging interface hbond scripts.
c596146
@jadolfbr
fix a bunch more plots with ggplot2 upgrade. fun stuff.
920a6a2
@jadolfbr
fix more crap that the new ggplot2 broke.
f11e4e9
@jadolfbr
fix more crap that the new ggplot2 broke.
e015f63
@jadolfbr
more fixes.
5357ee7
@jadolfbr
some trimming to scripts. Better filtering of low data.
1d41ab4
@jadolfbr
remove some unused interface features scripts. fix up.
1b5054d
@jadolfbr
finish fixing features scripts.
f853f3b
@jadolfbr
testing.
72274f3
@jadolfbr
fix top n percent plots to do ddplyr to correctly select top models.
fd6d311
@jadolfbr
fix top n percent plots to do ddplyr to correctly select top models.
55cc8db
@jadolfbr
fix top n percent plots to do ddplyr to correctly select top models.
cbb1238
@jadolfbr
fix top n percent plots to do ddplyr to correctly select top models.
acb4a28
@jadolfbr
fix top n percent plots to do ddplyr to correctly select top models.
2b27ece
@jadolfbr
fix top n percent plots to do ddplyr to correctly select top models.
6f0b3a9
@jadolfbr
remove lm plot from dG vs.
b00c382
@jadolfbr
add plots for total score testing by native.
e677412
@jadolfbr
add plots for total score testing by native.
e370958
@jadolfbr
add native plots.
b9414f9
@jadolfbr
add native plots.
1b12257
@jadolfbr
add native plots.
d03a9ab
@jadolfbr
add native plots.
6707544
@jadolfbr
add native plots.
036a1e5
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3 participants
@jadolfbr @rfalford12 @momeara