ClusterGrid layouts: fixing longstanding issues

[lukauskas]

This PR fixes a few of annoying things with sns.clustermap that have been there for since I remember.

Here's a detailed list with some examples

Fix 1: Fix the clustermap scaling with size: dendrogram should not scale

The heatmap scaling has been completely broken since forever.
The code claims that it is set up so only the heatmap scales, not the dendrogram, but this is not the case:

import seaborn as sns; sns.set(color_codes=True)
iris = sns.load_dataset("iris")
species = iris.pop("species")
lut = dict(zip(species.unique(), "rbg"))
row_colors = species.map(lut)

g = sns.clustermap(iris, row_colors=row_colors, figsize=(5, 5))
g = sns.clustermap(iris, row_colors=row_colors, figsize=(10, 5))
g = sns.clustermap(iris, row_colors=row_colors, figsize=(5, 10))

5,5:

10,5:

5,10:

With this PR, 10,5:

With this PR 5, 10:

Fix 2: prevent squashing of row_colors when multiple annotations are given

row_colors_multiple = pd.DataFrame({'foo': species.map(dict(zip(species.unique(), sns.color_palette('Set1', 3).as_hex()))),
                                    'bar': species.map(dict(zip(species.unique(), sns.color_palette('Set2', 3).as_hex()))),
                                    'baz': species.map(dict(zip(species.unique(), sns.color_palette('Set3', 3).as_hex()))),
                                    'boo': species.map(dict(zip(species.unique(), sns.color_palette('Dark2', 3).as_hex())))})
g = sns.clustermap(iris, row_colors=row_colors_multiple, figsize=(5, 5))

Before:

After:

Fix 3: Extend colorbar through the whole length of dendrogram and row_colors if provided

g = sns.clustermap(iris.T, col_colors=row_colors_multiple, figsize=(5, 5))

Before:

After:

Other things that are new

I've also added parameters to clustermap to allow to change the size of dendrogram and colors.

Unfortunately I didn't manage to fix clustermaps with square=True, these are still broken beyond repair.

[lukauskas]

@mwaskom , do you know what is happening here?

This is an odd place for the tests to fail as I did not touch color palettes...

=================================== FAILURES ===================================
____________________ TestColorPalettes.test_get_color_cycle ____________________
self = <seaborn.tests.test_palettes.TestColorPalettes object at 0x2af46b1cbed0>
    def test_get_color_cycle(self):
        with warnings.catch_warnings():
            warnings.simplefilter('ignore')
            result = utils.get_color_cycle()
>           expected = mpl.rcParams['axes.color_cycle']
seaborn/tests/test_palettes.py:296: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
self = RcParams({'_internal.classic_mode': False,
          'agg.path.chunksize': 0,
...e': False,
          'ytick.minor.width': 0.5,
          'ytick.right': False})
key = 'axes.color_cycle'
    def __getitem__(self, key):
        inverse_alt = None
        if key in _deprecated_map:
            alt_key, alt_val, inverse_alt = _deprecated_map[key]
            warnings.warn(self.msg_depr % (key, alt_key),
                          mplDeprecation)
            key = alt_key
    
        elif key in _deprecated_ignore_map:
            alt = _deprecated_ignore_map[key]
            warnings.warn(self.msg_depr_ignore % (key, alt),
                          mplDeprecation)
            key = alt
    
        elif key in _obsolete_set:
            warnings.warn(self.msg_obsolete % (key, ),
                          mplDeprecation)
            return None
    
>       val = dict.__getitem__(self, key)
E       KeyError: 'axes.color_cycle'
../../../miniconda/envs/testenv/lib/python2.7/site-packages/matplotlib/__init__.py:950: KeyError

[lukauskas]

This fixes #437

[mwaskom]

@mwaskom , do you know what is happening here?

Matplotlib changed the color_cycle to prop_cycle a while back and must have just dropped the old name completely. I have no idea what that test was trapping warnings, which otherwise would probably have made it clear that this was happening...

[lukauskas]

Sorry about the radio silence in the last few days.

@mwaskom - do you want me to fix this test?

[mwaskom]

@mwaskom - do you want me to fix this test?

No that shouldn't be part of this PR

[mwaskom]

See #1443

[dburkhardt]

What's the status on this PR? I would love to have access to these features!

[asalt]

What's the status on this PR? I would love to have access to these features!

@dburkhardt
Looks like in limbo while the future of clustermap and heatmap are in transition (see #1443 ). However, it's pretty easy to simply copy/paste the added functionality from this pull request into your own code. It's all pure Python, and easy to put into your own projects as an importable class.

class MyCluserGrid(seaborn.matrix.Clustergrid):
    def new_or_updated_function():
        # new code

This is probably easier than forking the entire repo.