Generate alpha diversity graphs for each metadata category of interest #209

            filename = '-'.join([name, cleaned_col]) + '.txt'

            with open(join(out_dir, filename), 'w') as f:
                for otu, val in zip(ids, table.data(col)):
                    if val == 0.0:
                        continue
                    f.write('%s\t%s\n' % (otu, str(val)))
+
+
+def cat_alpha_plots():


no unit test?

This generates images, and the core function generating the image is tested, so I'm not sure how to unit test this. Do you have suggestions?

Hmm how about computing the md5 (ex. self.assertFileMD5() in this package)? Otherwise simply verifying your output file (shannon_path, pd_path) exists as you expect?

Hesitant to do MD5 because it could be sliiiightly rendered differently depending on the system tests are run on. Checking file is output would work though, and also makes sure the proper naming for files is there so the website can use them. Adding that.

ekopylova · 2016-06-14T04:33:08Z

lualatex seems to be a dependency but don't see it mentioned anywhere

ekopylova · 2016-06-14T04:46:50Z

@squirrelo a few comments

squirrelo · 2016-06-14T15:25:02Z

The lualatex is needed for rendering the barcode results PDFs.

squirrelo · 2016-06-14T21:39:32Z

Test added for file names, but there is not a way to actually test the graph itself.

squirrelo · 2016-06-15T19:35:25Z

Travis is not behaving for testing the rendering, and given that there are no other tests for rendering in the codebase, how much of a priority/how imperative is it that we have the render tests, given we're not checking the figure that is rendered and instead just the filename.

josenavas · 2016-06-15T19:40:48Z

Just checked the error really fast. It looks like the error is saying that the label "70+" is not in the axis. I'm unsure on how the figure is generated and I understand that systems can change the output figure a bit. However, I think that changing the axis is not a small change and it should be ensure that the axis are as we expect. It may be a bit more helpful to see an example of the image generated attached in here.

squirrelo · 2016-06-15T19:42:48Z

That error is the latest in a long string of errors, mostly having to do with the latex not rendering correctly or at all. Only the latest non-working commit is in the PR for brevity's sake.

squirrelo · 2016-06-15T19:52:22Z

Here is an example graph:

squirrelo · 2016-06-15T21:34:09Z

Aaaand now tests are passing. Ok, cool.

josenavas · 2016-06-21T17:53:05Z

Code looks good - however, before merging, I'm gonna pulldown this code and test it using the latest AG round

squirrelo · 2016-06-23T15:31:06Z

ping @josenavas mergable?

josenavas · 2016-06-23T16:42:35Z

No it's not:

Exception: Traceback (most recent call last):
  File "/home/jona1883/software/American-Gut/americangut/parallel.py", line 27, in run_functor
    return functor(*args, **kwargs)
  File "/home/jona1883/software/American-Gut/americangut/per_sample.py", line 117, in sample_type_processor
    return merge_error_reports(*[f(opts, ids) for f in functions])
  File "/home/jona1883/software/American-Gut/americangut/per_sample.py", line 307, in alpha_plot
    fp=shannon_path)
  File "/home/jona1883/software/American-Gut/americangut/results_utils.py", line 730, in plot_alpha
    sample_alpha, group_alpha.mean()).expandtabs()
AttributeError: 'tuple' object has no attribute 'expandtabs'

I though you told me that you did not modify the plot alpha function?

squirrelo · 2016-06-23T17:30:04Z

The only change is to prepend the alpha diversity type, which we discussed offline. Investigating now.

On Jun 23, 2016, at 09:42, Jose Navas notifications@github.com wrote:

No it's not:

Exception: Traceback (most recent call last):
File "/home/jona1883/software/American-Gut/americangut/parallel.py", line 27, in run_functor
return functor(_args, _kwargs)
File "/home/jona1883/software/American-Gut/americangut/per_sample.py", line 117, in sample_type_processor
return merge_error_reports([f(opts, ids) for f in functions])
File "/home/jona1883/software/American-Gut/americangut/per_sample.py", line 307, in alpha_plot
fp=shannon_path)
File "/home/jona1883/software/American-Gut/americangut/results_utils.py", line 730, in plot_alpha
sample_alpha, group_alpha.mean()).expandtabs()
AttributeError: 'tuple' object has no attribute 'expandtabs'
I though you told me that you did not modify the plot alpha function?

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squirrelo · 2016-06-23T17:38:51Z

Fixed the issue. Was missing parenthesis.

squirrelo added 8 commits April 20, 2016 14:16

move plot_alpha to results_utils

12c736c

Merge branch 'generate-taxa-by-summary' into generate-alpha-diversity…

28223f3

…-per-sample

add cat_alpha_plot function

e250de9

add to notebook

7c91fd7

small rename

c82470f

fix imports

574452f

flake8

32b1b73

fix missing path

264551c

squirrelo changed the title ~~Generate alpha diversity graphs for each metadata category of interest~~ WIP: Generate alpha diversity graphs for each metadata category of interest Apr 21, 2016

squirrelo added 2 commits April 20, 2016 17:23

move alpha diversity files when completed

e128ed9

tweaks and bugfixes

a77eadd

remove _type from cat name

acac556

squirrelo changed the title ~~WIP: Generate alpha diversity graphs for each metadata category of interest~~ Generate alpha diversity graphs for each metadata category of interest Apr 25, 2016

squirrelo added 2 commits April 25, 2016 12:01

Fix file naming issue

1ccc137

Merge branch 'master' of https://github.com/biocore/American-Gut into…

b7ac4dc

… generate-alpha-diversity-per-sample

ekopylova reviewed Jun 14, 2016
View reviewed changes

squirrelo added 2 commits June 14, 2016 08:54

address comments

e1a7d3c

add test

454fa7c

squirrelo force-pushed the generate-alpha-diversity-per-sample branch 7 times, most recently from 02a524b to 8b65db1 Compare June 14, 2016 22:58

update travis

cf6cc45

squirrelo force-pushed the generate-alpha-diversity-per-sample branch from 8b65db1 to cf6cc45 Compare June 14, 2016 23:04

change plotted title

b80c938

move underscores

1f24ca0

squirrelo force-pushed the generate-alpha-diversity-per-sample branch from 2108b73 to 1f24ca0 Compare June 21, 2016 18:31

prefix to suffix

bbda36b

squirrelo closed this Jun 23, 2016

squirrelo reopened this Jun 23, 2016

parenthesis

5d68a8b

squirrelo closed this Apr 10, 2018

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Generate alpha diversity graphs for each metadata category of interest #209

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Generate alpha diversity graphs for each metadata category of interest #209

Generate alpha diversity graphs for each metadata category of interest #209

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