Adding 2d histogram function #5249

konradjk · 2019-02-05T02:57:20Z

No description provided.

konradjk · 2019-02-05T03:42:03Z

You're the lucky winner @jbloom22

~~Also, weird, the tests are failing, but in code I didn't write...~~

jbloom22 · 2019-02-06T02:54:07Z

hail/python/hail/plot/plots.py

@@ -126,6 +127,147 @@ def cumulative_histogram(data, range=None, bins=50, legend=None, title=None, nor
    return p


+def set_font_size(p, font_size: str = "12pt"):
+    """Set as many font sizes as possible in a bokeh figure


"Set all possible font sizes in a bokeh figure."

Well, I'm not 100% sure that these are all of the possible ones. Just the ones I've encountered so far. I'll make this a sub-function of the histogram2d one for now

jbloom22 · 2019-02-06T02:54:18Z

hail/python/hail/plot/plots.py

+    Parameters
+    ----------
+    p : :class:`bokeh.plotting.figure.Figure`
+        Input Figure.


lower-case figure

jbloom22 · 2019-02-06T02:55:07Z

hail/python/hail/plot/plots.py

+    p : :class:`bokeh.plotting.figure.Figure`
+        Input Figure.
+    font_size : str
+        String of font size in points (e.g. "12pt").


single-quote more pythonic?

jbloom22 · 2019-02-06T02:58:36Z

hail/python/hail/plot/plots.py

+                 plot_title='2-D histogram', plot_width=600, plot_height=600, font_size='7pt',
+                 colors=bokeh.palettes.all_palettes['Blues'][7][::-1]):
+    """Plot a 2-D histogram of x vs y, which are NumericExpressions from a Table.
+


Add Examples section illustrating how the parameters are used

We usually give examples in a section that starts with:

Examples ---------

e.g.
https://hail.is/docs/0.2/methods/impex.html#hail.methods.import_bgen

jbloom22 · 2019-02-06T02:59:45Z

hail/python/hail/plot/plots.py

+    check_row_indexed('histogram_2d', x)
+    check_row_indexed('histogram_2d', y)
+    if source != y_source:
+        raise ValueError(f"histogram_2d expects two expressions of 'Table', found {source} and {y_source}")


you mean, on the same table?

move this check up a couple lines

jbloom22 · 2019-02-06T03:02:56Z

hail/python/hail/plot/plots.py

+
+    grouped_ht = source.group_by(
+        x=hail.str(x_levels.find(lambda w: x >= w)), y=hail.str(y_levels.find(lambda w: y >= w))
+    ).aggregate(c=hail.agg.count())


is this the right indentation?

My PyCharm claims it is but happy to change if there's another preferred one

jbloom22 · 2019-02-06T03:04:07Z

hail/python/hail/plot/plots.py

+    font_size : str
+        String of font size in points (default "7pt").
+    colors : List[str]
+        List of hex colors from low to high.


Could you more explanation (or a link) regarding how this is used

jbloom22 · 2019-02-06T03:13:51Z

I think if there are elements outside the range you should warn

jbloom22 · 2019-02-06T03:14:41Z

hail/python/hail/plot/plots.py

+    y_levels = hail.literal(list(frange(y_range[0], y_range[1], y_spacing))[::-1])
+
+    grouped_ht = source.group_by(
+        x=hail.str(x_levels.find(lambda w: x >= w)), y=hail.str(y_levels.find(lambda w: y >= w))


why strings?

This is a little funky. Bokeh needs them to be strings in order to correctly plot them as discrete values rather than a continuous scale.

konradjk · 2019-02-06T14:14:48Z

Also willing to discuss a default color palette - anyone want to have a principled discussion about some nice defaults?

addressed

jbloom22

Just a few small tweaks, otherwise looks great!

jbloom22 · 2019-02-07T16:52:02Z

hail/python/hail/plot/plots.py

+           bins=int, x_bins=nullable(int), y_bins=nullable(int),
+           plot_title=nullable(str), plot_width=int, plot_height=int,
+           font_size=str, colors=sequenceof(str))
+def histogram_2d(x, y, x_range=None, y_range=None, bins=40, x_bins=None, y_bins=None,


numpy and matplotlib don't have the _. I'd remove it for consistency
https://docs.scipy.org/doc/numpy/reference/generated/numpy.histogram2d.html
https://matplotlib.org/api/_as_gen/matplotlib.pyplot.hist2d.html

jbloom22 · 2019-02-07T16:52:45Z

hail/python/hail/plot/plots.py

+def histogram_2d(x, y, x_range=None, y_range=None, bins=40, x_bins=None, y_bins=None,
+                 plot_title='2-D histogram', plot_width=600, plot_height=600, font_size='7pt',
+                 colors=bokeh.palettes.all_palettes['Blues'][7][::-1]):
+    """Plot a 2-D histogram.


Plot a two-dimensional histogram.

jbloom22 · 2019-02-07T16:53:38Z

hail/python/hail/plot/plots.py

+                 plot_title='2-D histogram', plot_width=600, plot_height=600, font_size='7pt',
+                 colors=bokeh.palettes.all_palettes['Blues'][7][::-1]):
+    """Plot a 2-D histogram of x vs y, which are NumericExpressions from a Table.
+


We usually give examples in a section that starts with:

Examples ---------

e.g.
https://hail.is/docs/0.2/methods/impex.html#hail.methods.import_bgen

jbloom22 · 2019-02-07T16:54:07Z

hail/python/hail/plot/plots.py

+        Number of bins on x-axis, will override ``bins`` if provided.
+    y_bins : int
+        Number of bins on y-axis, will override ``bins`` if provided.
+    plot_width : int


why prefix these three with plot?

jbloom22 · 2019-02-07T16:54:37Z

hail/python/hail/plot/plots.py

+        String of font size in points (default '7pt').
+    colors : List[str]
+        List of colors (hex codes, or strings as described
+        `here <https://bokeh.pydata.org/en/latest/docs/reference/colors.html>`__). Effective with one of the many


"Compatible" rather than "Effective"?

addressed

Adding 2d histogram function

9b18c9f

konradjk assigned jbloom22 Feb 5, 2019

konradjk added 6 commits February 4, 2019 22:45

added typecheck and into index

641ae33

removing typehints

8b75f93

bugfix

895db58

fix for when range is provided and some values are below minimum

e8db66f

idk why this was reversed

b4a0ac7

picked a more color-blind friendly palette (darkening blues)

d0a53c1

jbloom22 previously requested changes Feb 6, 2019

View reviewed changes

jbloom22 reviewed Feb 6, 2019

View reviewed changes

konradjk added 2 commits February 6, 2019 08:56

addressed most comments

22d46d3

expressly removing points outside bounds

9e2c5b3

konradjk added 4 commits February 6, 2019 12:26

doc fixes, added example

ffb030f

bugfix

8db275e

added example to plotting tutorial

1c4b7ab

fix for an older version of bokeh than required by hail

29849b5

konradjk added 4 commits February 6, 2019 18:43

fix tooltip, docstring cleanup

71c2c11

describing plotting tutorial

cda40ac

Merge branch 'master' into hist2d

3398899

docfix

8949d05

jbloom22 previously requested changes Feb 7, 2019

View reviewed changes

addressed comments, consolidated range and bins arguments

34767ce

removed underscore from name

5605cf6

jbloom22 approved these changes Feb 7, 2019

View reviewed changes

moving title font size out if none exists

567243a

list to tuple

d25eabf

danking merged commit c3b1183 into hail-is:master Feb 8, 2019

konradjk deleted the hist2d branch February 8, 2019 14:19

This was referenced Apr 29, 2024

Hail 0.2.10 patch notes iris-garden/test-process#1662

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Adding 2d histogram function #5249

Adding 2d histogram function #5249

konradjk commented Feb 5, 2019

konradjk commented Feb 5, 2019 •

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Adding 2d histogram function #5249

Adding 2d histogram function #5249

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konradjk commented Feb 5, 2019

konradjk commented Feb 5, 2019 • edited Loading

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jbloom22 commented Feb 6, 2019

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konradjk commented Feb 6, 2019

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konradjk commented Feb 5, 2019 •

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