def test_plot_sums(self, test_insertions, test_exon_counts):
"""Exercises plotting of sums."""
result = test.test_de_exon(test_insertions,
test_exon_counts,
gene_id='ENSMUSG00000026510')
result.plot_sums()
def plot_de(insertions,
exon_counts,
gene_id,
gene_name=None,
ax=None,
box_kws=None,
strip_kws=None,
**kwargs):
"""Plots groupwise DE for a given gene."""
if gene_name is None:
gene_name = gene_id
result = test_de_exon(insertions, exon_counts, gene_id=gene_id, **kwargs)
if result.p_value <= 0.05:
if result.direction == 1:
color = sns.color_palette('Set1')[2] # Green
else:
color = sns.color_palette('Set1')[3] # Purple
else:
color = 'lightgrey'
ax = result.plot_boxplot(ax=ax,
log=True,
show_points=True,
strip_kws=strip_kws or {},
box_kws=toolz.merge({'color': color}, box_kws
or {}))
pval_label = _format_pval(result.p_value)
ax.set_title('{} ({})'.format(gene_name, pval_label), fontstyle='italic')
return ax
def test_neg_example_nf1(self, test_insertions, test_exon_counts):
"""Tests negative example of DE in Nf1 in the SB dataset."""
result = test.test_de_exon(
test_insertions, test_exon_counts, gene_id='ENSMUSG00000020716')
assert result.p_value > 0.05
assert result.direction == 1
def test_pos_example_trp53bp2(self, test_insertions, test_exon_counts):
"""Tests positive example of DE in Trp53bp2 in the SB dataset."""
result = test.test_de_exon(
test_insertions, test_exon_counts, gene_id='ENSMUSG00000026510')
assert result.p_value < 0.01
assert result.direction == 1
def test_neg_example_nf1(self, test_insertions, test_exon_counts):
"""Tests negative example of DE in Nf1 in the SB dataset."""
result = test.test_de_exon(test_insertions,
test_exon_counts,
gene_id='ENSMUSG00000020716')
assert result.p_value > 0.05
assert result.direction == 1
def test_pos_example_trp53bp2(self, test_insertions, test_exon_counts):
"""Tests positive example of DE in Trp53bp2 in the SB dataset."""
result = test.test_de_exon(test_insertions,
test_exon_counts,
gene_id='ENSMUSG00000026510')
assert result.p_value < 0.01
assert result.direction == 1
def test_pos_example_trp53bp2_df(self, test_insertions, test_exon_counts):
"""Tests positive example of DE in Trp53bp2 with dataframe input."""
test_insertion_df = Insertion.to_frame(test_insertions)
result = test.test_de_exon(
test_insertion_df, test_exon_counts, gene_id='ENSMUSG00000026510')
assert result.p_value < 0.01
assert result.direction == 1
def test_pos_example_trp53bp2_df(self, test_insertions, test_exon_counts):
"""Tests positive example of DE in Trp53bp2 with dataframe input."""
test_insertion_df = Insertion.to_frame(test_insertions)
result = test.test_de_exon(test_insertion_df,
test_exon_counts,
gene_id='ENSMUSG00000026510')
assert result.p_value < 0.01
assert result.direction == 1
def test_plot_sums(self, test_insertions, test_exon_counts):
"""Exercises plotting of sums."""
result = test.test_de_exon(
test_insertions, test_exon_counts, gene_id='ENSMUSG00000026510')
result.plot_sums()