Added heatmap plotting method to Alignment (and tests). #779

kestrelgorlick · 2014-11-25T00:23:20Z

Fixes #765

Based on @gregcaporaso's scikit-bio cookbook recipe:

http://nbviewer.ipython.org/github/biocore/scikit-bio-cookbook/blob/master/Alignment%20viewing%20and%20filtering.ipynb

@gregcaporaso

Fixes scikit-bio#765 Based on @gregcaporaso's scikit-bio cookbook recipe: http://nbviewer.ipython.org/github/biocore/scikit-bio-cookbook/blob/master/Alignment%20viewing%20and%20filtering.ipynb

coveralls · 2014-11-25T00:51:43Z

Coverage increased (+0.0%) when pulling 5f3b0b8 on Kleptobismol:issue-765 into 3df9544 on biocore:master.

coveralls · 2014-11-25T01:06:05Z

Coverage increased (+0.0%) when pulling cf79a1f on Kleptobismol:issue-765 into 3df9544 on biocore:master.

gregcaporaso · 2014-11-25T03:38:36Z

Thanks @Kleptobismol, looking forward to trying this out!

jairideout · 2014-11-25T15:15:36Z

Thanks @Kleptobismol, I'll take a pass through later today.

jairideout · 2014-12-02T17:12:45Z

CHANGELOG.md

@@ -9,7 +9,7 @@
 * Added `skbio.stats.power` for performing emperical power analysis. The module uses existing datasets and iteratively draws samples to estimate the number of samples needed to see a significant difference for a given critical value.
 * Added `skbio.stats.isubsample` for subsampling from an unknown number of values. This method supports subsampling from multiple partitions and does not require that all items be stored in memory, requiring approximately `O(N*M)`` space where `N` is the number of partitions and `M` is the maximum subsample size.
 * Added ``skbio.stats.subsample_counts``, which replaces ``skbio.stats.subsample``. See deprecation section below for more details ([#770](https://github.com/biocore/scikit-bio/issues/770)).
-
+* Added ``heatmap`` method to ``skbio.alignment.Alignment`` for creating a heatmap from an alignment (see [#765](https://github.com/biocore/scikit-bio/issues/765)).


add a newline below here to separate this section from the bug fixes section

ElDeveloper · 2014-12-02T17:46:53Z

This may be a rather general comment but is there a reason why this method doesn't use seaborn to produce the heat map? See this link.

cc @gregcaporaso

gregcaporaso · 2014-12-02T20:23:46Z

I think using seaborn.heatmap would be a good idea, but that could also be changed in another PR if this is close to merge.

jairideout · 2014-12-03T17:07:43Z

👍 for using seaborn. Let's get this merged first and then update all of the existing plotting methods to use seaborn in another pull request (Alignment, DissimilarityMatrix, and OrdinationResults).

Also fig_size defaults to None, and so does cmap.

coveralls · 2014-12-04T00:19:43Z

Coverage increased (+0.0%) when pulling 7f52bcb on Kleptobismol:issue-765 into 3df9544 on biocore:master.

coveralls · 2014-12-05T18:26:00Z

Coverage decreased (-0.15%) when pulling 2e5b21b on Kleptobismol:issue-765 into 3df9544 on biocore:master.

jairideout · 2014-12-07T23:26:46Z

skbio/alignment/_alignment.py

@@ -1668,6 +1671,125 @@ def to_phylip(self, map_labels=False, label_prefix=""):

        return '\n'.join(result), new_id_to_old_id

+    def heatmap(self, value_map, legend_labels=['Minimum', 'Median',


Sorry I didn't catch this before: the default value for legend_labels should be changed to a tuple instead of a list (see here for an explanation why).

jairideout · 2014-12-08T01:06:31Z

@Kleptobismol done reviewing

kestrelgorlick · 2014-12-14T16:05:30Z

What variable should I be passing to np.empty? It says it requires a "shape" argument (pos1)

kestrelgorlick · 2014-12-14T16:14:58Z

nevermind it's between sequence_length and sequence_count

The docstring entries about the X and Y axis labels are likely in the wrong place.

kestrelgorlick · 2014-12-14T16:56:02Z

What do i do about this?
Warning, treated as error:
WARNING: intersphinx inventory 'http://docs.python.org/dev/objects.inv' not fetchable due to <class 'urllib2.URLError'>: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:581)>

ebolyen · 2014-12-15T14:48:53Z

@Kleptobismol That happens when travis has a network error. I'm rerunning the tests, they should pass fine this time.

ebolyen · 2014-12-15T15:05:50Z

Strange, the python3 test loads the docs fine, but the tests fail. Python2 the tests succeed, but the docs won't load.

kestrelgorlick · 2014-12-15T17:26:14Z

So i didn't do anything wrong?
I am coming to the code sprint around 4 today so maybe we can quickly discuss this there @ebolyen

coveralls · 2014-12-16T01:45:27Z

Coverage decreased (-0.03%) when pulling c29d54f on Kleptobismol:issue-765 into ddbb3dd on biocore:master.

jairideout · 2014-12-30T18:21:28Z

CHANGELOG.md

@@ -11,6 +11,7 @@
 * Added `skbio.stats.power` for performing empirical power analysis. The module uses existing datasets and iteratively draws samples to estimate the number of samples needed to see a significant difference for a given critical value.
 * Added `skbio.stats.isubsample` for subsampling from an unknown number of values. This method supports subsampling from multiple partitions and does not require that all items be stored in memory, requiring approximately `O(N*M)`` space where `N` is the number of partitions and `M` is the maximum subsample size.
 * Added ``skbio.stats.subsample_counts``, which replaces ``skbio.stats.subsample``. See deprecation section below for more details ([#770](https://github.com/biocore/scikit-bio/issues/770)).
+* Added ``heatmap`` method to ``skbio.alignment.Alignment`` for creating a heatmap from an alignment (see [#765](https://github.com/biocore/scikit-bio/issues/765)).


Can you please move this under a Features heading in the 0.2.2-dev section?

jairideout · 2014-12-30T18:51:57Z

@Kleptobismol I took another pass through, please see my comments inline. Thanks!

coveralls · 2015-01-09T17:21:26Z

Coverage decreased (-0.05%) when pulling 1cf2e9f on Kleptobismol:issue-765 into ddbb3dd on biocore:master.

coveralls · 2015-01-13T20:11:27Z

Coverage increased (+0.04%) when pulling 6fa40a8 on Kleptobismol:issue-765 into ddbb3dd on biocore:master.

jairideout · 2015-02-09T17:46:00Z

@Kleptobismol sorry for the delay on this. I'm pulling your commits to make some minor edits and to play around with the code a bit. I'll submit a new pull request sometime today that has your commits plus my changes.

jairideout · 2015-02-11T18:52:51Z

Closing in favor of #816.

kestrelgorlick added 2 commits November 24, 2014 17:10

Added heatmap plotting method to Alignment (and tests).

426a3f6

Fixes scikit-bio#765 Based on @gregcaporaso's scikit-bio cookbook recipe: http://nbviewer.ipython.org/github/biocore/scikit-bio-cookbook/blob/master/Alignment%20viewing%20and%20filtering.ipynb

Addresses @Jorge-C's comment regarding matplotlib.pyplot import.

c6c8d6e

jairideout added this to the 0.2.2: Easy as ABC milestone Nov 25, 2014

kestrelgorlick added 3 commits November 24, 2014 17:29

Added my alignment heatmap method to the changelog.

5f9d989

Fixes Travis plotting errors.

5f3b0b8

Cleaned up docstring.

cf79a1f

jairideout self-assigned this Nov 25, 2014

jairideout reviewed Dec 2, 2014
View reviewed changes

kestrelgorlick added 3 commits December 3, 2014 16:32

Addresses @jairideout's comments.

fc6015c

Also fig_size defaults to None, and so does cmap.

Fixes Travis errors.

d51d603

Fixes Travis error.

7f52bcb

Cleaned up tests and added a few lines to _alignment.py .

2e5b21b

jairideout reviewed Dec 7, 2014
View reviewed changes

Addresses @jairideout's comments

42989b7

The docstring entries about the X and Y axis labels are likely in the wrong place.

kestrelgorlick added 2 commits December 15, 2014 18:28

Fixed Travis error

6ab20c0

Merge branch 'master' into issue-765

c29d54f

jairideout reviewed Dec 30, 2014
View reviewed changes

Addresses @jairideout's comments

1cf2e9f

Adds tests in order to fix coverage loss.

6fa40a8

jairideout mentioned this pull request Feb 11, 2015

ENH: add Alignment.heatmap method #816

Closed

jairideout closed this Feb 11, 2015

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Added heatmap plotting method to Alignment (and tests). #779

Added heatmap plotting method to Alignment (and tests). #779

kestrelgorlick commented Nov 25, 2014

coveralls commented Nov 25, 2014

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gregcaporaso commented Nov 25, 2014

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jairideout commented Feb 11, 2015

		@@ -1668,6 +1671,125 @@ def to_phylip(self, map_labels=False, label_prefix=""):

		return '\n'.join(result), new_id_to_old_id

		def heatmap(self, value_map, legend_labels=['Minimum', 'Median',

Added heatmap plotting method to Alignment (and tests). #779

Added heatmap plotting method to Alignment (and tests). #779

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kestrelgorlick commented Nov 25, 2014

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