def test_filter_subsets(min, max):
data = generate_samples(0, 5000, 3)
upset_data = UpSet(data, subset_size='auto')
subset_upset_data = UpSet(data,
subset_size='auto',
min_subset_size=min,
max_subset_size=max)
intersections = upset_data.intersections
df = upset_data._df
subset_intersections = intersections[np.logical_and(
intersections >= min, intersections <= max)]
subset_df = df[df.index.isin(subset_intersections.index)]
assert_series_equal(subset_upset_data.intersections, subset_intersections)
def _pack_binary(X):
X = pd.DataFrame(X)
out = 0
for i, (_, col) in enumerate(X.items()):
out *= 2
out += col
return out
subset_df_packed = _pack_binary(subset_df.index.to_frame())
subset_data_packed = _pack_binary(subset_intersections.index.to_frame())
subset_df['_bin'] = pd.Series(subset_df_packed).map(
pd.Series(np.arange(len(subset_data_packed)),
index=subset_data_packed))
assert_frame_equal(subset_upset_data._df, subset_df)
def Venn_Upset(adata,genelists,size_height=3):
from upsetplot import UpSet
from upsetplot import plot
#gene lists can be ['Deep_1','Deep_2']
deepgenes=pd.DataFrame(adata.var[genelists+['highly_variable']])
deepgenes=deepgenes.set_index(genelists)
upset = UpSet(deepgenes, subset_size='count', intersection_plot_elements=size_height)
upset.plot()
return upset
def UpSetFromLists(listOflist,labels,size_height=3,showplot=True):
from upsetplot import UpSet
listall=list(set([j for i in listOflist for j in i]))
temp=pd.Series(listall,index=listall)
temp2=pd.concat([temp.isin(i) for i in listOflist+[temp]],axis=1)
temp2.columns=labels+['all']
temp2=temp2.set_index(labels)
upset = UpSet(temp2,subset_size='count', intersection_plot_elements=3)
if showplot is True:
upset.plot()
return upset
def test_index_must_be_bool(x):
# Truthy ints are okay
x = x.reset_index()
x[['cat0', 'cat2', 'cat2']] = x[['cat0', 'cat1', 'cat2']].astype(int)
x = x.set_index(['cat0', 'cat1', 'cat2']).iloc[:, 0]
UpSet(x)
# other ints are not
x = x.reset_index()
x[['cat0', 'cat2', 'cat2']] = x[['cat0', 'cat1', 'cat2']] + 1
x = x.set_index(['cat0', 'cat1', 'cat2']).iloc[:, 0]
with pytest.raises(ValueError, match='not boolean'):
UpSet(x)
def plot_upset(sets, path):
if len(sets) > 1:
df_upset = from_contents(sets)
upset_plot = UpSet(df_upset,
sort_by='degree',
sort_categories_by='cardinality',
show_counts=True,
show_percentages=True)
fig = plt.figure()
upset_plot.plot(fig=fig)
fig.savefig(path)
elif len(sets) in {0, 1}:
print(f'plot_upset: No sets to intersect for {path}')
def test_vertical():
X = generate_data(n_samples=100)
fig = matplotlib.figure.Figure()
UpSet(X, orientation='horizontal').make_grid(fig)
horz_height = fig.get_figheight()
horz_width = fig.get_figwidth()
assert horz_height < horz_width
fig = matplotlib.figure.Figure()
UpSet(X, orientation='vertical').make_grid(fig)
vert_height = fig.get_figheight()
vert_width = fig.get_figwidth()
assert horz_width / horz_height > vert_width / vert_height
# TODO: test axes positions, plot order, bar orientation
pass
def test_element_size():
X = generate_data(n_samples=100)
figsizes = []
for element_size in range(10, 50, 5):
fig = matplotlib.figure.Figure()
UpSet(X, element_size=element_size).make_grid(fig)
figsizes.append((fig.get_figwidth(), fig.get_figheight()))
figwidths, figheights = zip(*figsizes)
# Absolute width increases
assert np.all(np.diff(figwidths) > 0)
aspect = np.divide(figwidths, figheights)
# Font size stays constant, so aspect ratio decreases
assert np.all(np.diff(aspect) < 0)
# But doesn't decrease by much
assert np.all(aspect[:-1] / aspect[1:] < 1.1)
fig = matplotlib.figure.Figure()
figsize_before = fig.get_figwidth(), fig.get_figheight()
UpSet(X, element_size=None).make_grid(fig)
figsize_after = fig.get_figwidth(), fig.get_figheight()
assert figsize_before == figsize_after
def test_sort_sets_by_deprecation(x, sort_sets_by):
with pytest.warns(DeprecationWarning, match='sort_sets_by'):
upset1 = UpSet(x, sort_sets_by=sort_sets_by)
with pytest.warns(None):
upset2 = UpSet(x, sort_categories_by=sort_sets_by)
fig = matplotlib.figure.Figure()
upset1.plot(fig)
png1 = io.BytesIO()
fig.savefig(png1, format='raw')
fig = matplotlib.figure.Figure()
upset2.plot(fig)
png2 = io.BytesIO()
fig.savefig(png2, format='raw')
assert png1.getvalue() == png2.getvalue()
def plot_intersection(data: dict, plot_outfile: str = "upsetplot.pdf"):
"""
Take a dict of lists of unique identifiers, make quantitative venn diagram.
Arguments:
(REQUIRED) data: dict of lists, transformed with from_contents
(OPTIONAL) plot_outfile: save the figure here
"""
data = UpSet(data,
show_counts=True,
show_percentages=True,
sort_categories_by=None)
data.plot()
if plot_outfile:
plt.savefig(plot_outfile)
else:
plt.show()
def upsetplot_miss(data):
null_cols_df = data.loc[:, data.isnull().any()]
missingness = pd.isna(null_cols_df).rename(columns=lambda x: x + '_NA')
for i, col in enumerate(missingness.columns):
null_cols_df = null_cols_df.set_index(missingness[col], append=i != 0)
tuple_false_values = (False, ) * sum(data.isnull().any())
null_cols_only_miss_df = null_cols_df.loc[
null_cols_df.index != tuple_false_values, :]
upset = UpSet(null_cols_only_miss_df,
subset_size='count',
show_counts=True,
sort_by='cardinality')
return (upset)
def lp_dist(data, percentage=False, scale=1, fname=None):
"""Plot pattern combination frequencies as an UpSet plot.
Parameters
----------
data : AnnData
Spatial formatted AnnData
percentage : bool, optional
If True, label each bar as a percentage else label as a count, by default False
scale : int, optional
scale > 1 scales the plot larger, scale < 1 scales. the plot smaller, by default 1
fname : str, optional
Save the figure to specified filename, by default None
"""
sample_labels = []
for p in PATTERN_NAMES:
p_df = data.to_df(p).reset_index().melt(id_vars="cell")
p_df = p_df[~p_df["value"].isna()]
p_df = p_df.set_index(["cell", "gene"])
sample_labels.append(p_df)
sample_labels = pd.concat(sample_labels, axis=1) == 1
sample_labels = sample_labels == 1
sample_labels.columns = PATTERN_NAMES
# Drop unlabeled samples
# sample_labels = sample_labels[sample_labels.sum(axis=1) > 0]
# Sort by degree, then pattern name
sample_labels["degree"] = -sample_labels[PATTERN_NAMES].sum(axis=1)
sample_labels = (sample_labels.reset_index().sort_values(
["degree"] + PATTERN_NAMES, ascending=False).drop("degree", axis=1))
upset = UpSet(
from_indicators(PATTERN_NAMES, data=sample_labels),
element_size=scale * 40,
min_subset_size=sample_labels.shape[0] * 0.001,
facecolor="lightgray",
sort_by=None,
show_counts=(not percentage),
show_percentages=percentage,
)
for p, color in zip(PATTERN_NAMES, PATTERN_COLORS):
if sample_labels[p].sum() > 0:
upset.style_subsets(present=p, max_degree=1, facecolor=color)
upset.plot()
plt.suptitle(
f"Localization Patterns\n{data.n_obs} cells, {data.n_vars} genes")
def plotUpset(adata,
study_col=None,
ct_col=None,
mn_key="MetaNeighborUS",
metaclusters="MetaNeighborUS_1v1_metaclusters",
outlier_label="outliers",
show=True):
"""Plot UpSet plot for intersections between datasets and metaclusters
Shows how replicability depends on hte input dataset
Arguments:
adata {AnnData} -- AnnData object containing the output of MetaNeighborUS 1vBest, and extractMetaClusters
Keyword Arguments:
study_col {[type]} -- If None, inferrefed from adata.uns[f'{mn_key}_params']['study_col'] else passed as vector (default: {None})
ct_col {[type]} -- If None, inferrefed from adata.uns[f'{mn_key}_params']['ct_col'] else passed as vector (default: {None})
mn_key {str} -- Location of MetaNeighborUS results (default: {'MetaNeighborUS'})
metaclusters {str} -- Location of extractMetaClusters results (default: {'MetaNeighborUS_1v1_metaclusters'})
outlier_label {str} -- Name of outlier_label in metaclusters (extractMetaClusters results) (default: {'outliers'})
show {bool} -- Flag for showing plot or return UpSet object (default: {True})
"""
if study_col is None:
study_col = adata.uns[f"{mn_key}_params"]["study_col"]
else:
assert study_col in adata.obs_keys(), "Study Col not in adata"
if ct_col is None:
ct_col = adata.uns[f"{mn_key}_params"]["ct_col"]
else:
assert ct_col in adata.obs_keys(), "Cluster Col not in adata"
if type(metaclusters) is str:
assert (metaclusters in adata.uns_keys()
), "Run extractMetaClusters or pass Metacluster Series"
metaclusters = adata.uns[metaclusters]
pheno, _, _ = create_cell_labels(adata, study_col, ct_col)
pheno = pheno.drop_duplicates().set_index("study_ct")
get_studies = lambda x: pheno.loc[x, study_col].values.tolist()
studies = [get_studies(x) for x in metaclusters.values]
membership = dict(zip(metaclusters.index, studies))
df = pd.DataFrame(
[{name: True
for name in names} for names in membership.values()],
index=membership.keys(),
)
df = df.fillna(False)
df = df[df.index != outlier_label]
df = df.groupby(df.columns.tolist(), as_index=False).size()
if type(
df
) is not pd.Series: #For pandas versions <1.0.0 size returns the correct series
cols = df.columns[:-1].copy()
for col in cols:
df.set_index(df[col], append=True, inplace=True)
df.index = df.index.droplevel(0)
df = df["size"]
us = UpSet(df, sort_by="cardinality")
if show:
plt.show()
else:
return us
def test_add_catplot():
pytest.importorskip('seaborn')
X = generate_data(n_samples=100)
upset = UpSet(X)
# smoke test
upset.add_catplot('violin')
fig = matplotlib.figure.Figure()
upset.plot(fig)
# can't provide value with Series
with pytest.raises(ValueError):
upset.add_catplot('violin', value='foo')
# check the above add_catplot did not break the state
upset.plot(fig)
X = generate_data(n_samples=100)
X.name = 'foo'
X = X.to_frame()
upset = UpSet(X, sum_over=False)
# must provide value with DataFrame
with pytest.raises(ValueError):
upset.add_catplot('violin')
upset.add_catplot('violin', value='foo')
with pytest.raises(ValueError):
# not a known column
upset.add_catplot('violin', value='bar')
upset.plot(fig)
# invalid plot kind raises error when plotting
upset.add_catplot('foobar', value='foo')
with pytest.raises(AttributeError):
upset.plot(fig)
from matplotlib import pyplot as plt
from upsetplot import UpSet
# Load the dataset into a DataFrame
boston = load_boston()
boston_df = pd.DataFrame(boston.data, columns=boston.feature_names)
# Get five features most correlated with median house value
correls = boston_df.corrwith(pd.Series(boston.target),
method='spearman').sort_values()
top_features = correls.index[-5:]
# Get a binary indicator of whether each top feature is above average
boston_above_avg = boston_df > boston_df.median(axis=0)
boston_above_avg = boston_above_avg[top_features]
boston_above_avg = boston_above_avg.rename(columns=lambda x: x + '>')
# Make this indicator mask an index of boston_df
boston_df = pd.concat([boston_df, boston_above_avg], axis=1)
boston_df = boston_df.set_index(list(boston_above_avg.columns))
# Also give us access to the target (median house value)
boston_df = boston_df.assign(median_value=boston.target)
# UpSet plot it!
upset = UpSet(boston_df, sum_over=False, intersection_plot_elements=3)
upset.add_catplot(value='median_value', kind='strip', color='blue')
upset.add_catplot(value='AGE', kind='strip', color='black')
upset.plot()
plt.show()
def test_param_validation(kw):
X = generate_data(n_samples=100)
with pytest.raises(ValueError):
UpSet(X, **kw)
x_df_3_binary = x_df_3_binary.set_index(selected_genes)
y_ind = y > 0
x_df_mets_3 = x_df_3.T[y_ind].T
x_df_mets_3_binary = x_df_mets_3.T > 0.
print x_df_mets_3_binary.shape
x_df_mets_3_binary = x_df_mets_3_binary.set_index(selected_genes)
font = {'family': 'Arial', 'weight': 'normal', 'size': 5}
matplotlib.rc('font', **font)
dd = x_df_3_binary.reset_index().set_index(['AR', 'TP53', 'MDM4'])
upset = UpSet(dd,
subset_size='count',
intersection_plot_elements=6,
show_counts=True,
with_lines=True,
element_size=10)
fig = plt.figure(constrained_layout=False, figsize=(8, 6))
upset.plot(fig)
fig.subplots_adjust(bottom=0.2, top=0.9, left=0.08, right=0.99)
saving_dir = join(PLOTS_PATH, 'figure4')
filename = join(saving_dir, 'figure4_ar_tp53_mdm4.png')
plt.savefig(filename, dpi=300)
matplotlib.rcParams['pdf.fonttype'] = 42
filename = join(saving_dir, 'figure4_ar_tp53_mdm4.pdf')
plt.savefig(filename)
top_features = correls.index[-5:]
# Get a binary indicator of whether each top feature is above average
boston_above_avg = boston_df > boston_df.median(axis=0)
boston_above_avg = boston_above_avg[top_features]
boston_above_avg = boston_above_avg.rename(columns=lambda x: x + '>')
# Make this indicator mask an index of boston_df
boston_df = pd.concat([boston_df, boston_above_avg], axis=1)
boston_df = boston_df.set_index(list(boston_above_avg.columns))
# Also give us access to the target (median house value)
boston_df = boston_df.assign(median_value=boston.target)
# UpSet plot it!
upset = UpSet(boston_df, subset_size='count', intersection_plot_elements=3)
upset.add_catplot(value='median_value', kind='strip', color='blue')
upset.add_catplot(value='AGE', kind='strip', color='black')
upset.plot()
plt.title("UpSet with catplots, for orientation='horizontal'")
plt.show()
# And again in vertical orientation
upset = UpSet(boston_df,
subset_size='count',
intersection_plot_elements=3,
orientation='vertical')
upset.add_catplot(value='median_value', kind='strip', color='blue')
upset.add_catplot(value='AGE', kind='strip', color='black')
upset.plot()
def gen_upset_plot(self, className=None):
# total_peps = len([pep for s in self.results.samples for pep in s.peptides])
total_peps = np.sum([len(s.peptides) for s in self.results.samples])
data = from_contents({s.sample_name: set(s.peptides)
for s in self.results.samples})
for intersection in data.index.unique():
if len(data.loc[intersection, :])/total_peps < 0.005:
data.drop(index=intersection, inplace=True)
data['peptide_length'] = np.vectorize(len)(data['id'])
n_sets = len(data.index.unique())
if n_sets <= 100: # Plot horizontal
upset = UpSet(data,
sort_by='cardinality',
#sort_categories_by=None,
show_counts=True,)
#totals_plot_elements=4,
#intersection_plot_elements=10)
upset.add_catplot(value='peptide_length', kind='boxen', color='gray')
plot = upset.plot()
plot['totals'].grid(False)
ylim = plot['intersections'].get_ylim()[1]
plot['intersections'].set_ylim((0, ylim * 1.1))
for c in plot['intersections'].get_children():
if isinstance(c, plotText):
text = c.get_text()
text = text.replace('\n', ' ')
c.set_text(text)
c.set_rotation('vertical')
pos = c.get_position()
pos = (pos[0], pos[1] + 0.02 * ylim)
c.set_position(pos)
else: # plot vertical
upset = UpSet(data, subset_size='count',
orientation='vertical',
sort_by='cardinality',
sort_categories_by=None,
show_counts=True)
upset.add_catplot(value='peptide_length', kind='boxen', color='gray')
plot = upset.plot()
lim = plot['intersections'].get_xlim()
plot['intersections'].set_xlim([0, lim[1] * 1.6])
plot['totals'].grid(False)
ylim = plot['totals'].get_ylim()[1]
for c in plot['totals'].get_children():
if isinstance(c, plotText):
text = c.get_text()
text = text.replace('\n', ' ')
c.set_text(text)
c.set_rotation('vertical')
pos = c.get_position()
pos = (pos[0], pos[1] + 0.1 * ylim)
c.set_position(pos)
plt.draw()
upset_fig = f'{self.fig_dir / "upsetplot.svg"}'
plt.savefig(upset_fig, bbox_inches="tight")
encoded_upset_fig = base64.b64encode(open(upset_fig, 'rb').read()).decode()
card = div(className='card', style="height: 100%")
card.add(div([b('UpSet Plot'), p('Only intersections > 0.5% are displayed')], className='card-header'))
plot_body = div(img(src=f'data:image/svg+xml;base64,{encoded_upset_fig}',
className='img-fluid',
style=f'width: 100%; height: auto'),
className='card-body')
card.add(plot_body)
return div(card, className=className)
