def test_edgeR_paired(self):
df = self._get_tuch_data()
ddf = DelayedDataFrame("ex1", df)
gts = {
"T": [x for x in sorted(df.columns) if ".T" in x],
"N": [x for x in sorted(df.columns) if ".N" in x],
}
c = Comparisons(ddf, gts)
a = c.a_vs_b("T", "N", EdgeRPaired())
force_load(ddf.add_annotator(a))
run_pipegraph()
# these are from the last run - the manual has no simple a vs b comparison...
# at least we'l notice if this changes
assert ddf.df[ddf.df.nameOfGene == "PTHLH"][
a["log2FC"]].values == approx([3.97], abs=1e-3)
assert ddf.df[ddf.df.nameOfGene == "PTHLH"][a["FDR"]].values == approx(
[4.27e-18])
assert ddf.df[ddf.df.nameOfGene == "PTHLH"][a["p"]].values == approx(
[8.13e-22])
df = ddf.df.set_index("nameOfGene")
t_columns = [x[1] for x in gts["T"]]
n_columns = [x[1] for x in gts["N"]]
assert df.loc["PTHLH"][t_columns].sum(
) > df.loc["PTHLH"][n_columns].sum()
assert ddf.df[ddf.df.nameOfGene == "PTGFR"][
a["log2FC"]].values == approx([-5.18], abs=1e-2)
assert ddf.df[ddf.df.nameOfGene == "PTGFR"][a["FDR"]].values == approx(
[3.17e-19])
assert ddf.df[ddf.df.nameOfGene == "PTGFR"][a["p"]].values == approx(
[3.01e-23])
assert df.loc["PTGFR"][t_columns].sum(
) < df.loc["PTGFR"][n_columns].sum()
def test_volcano_plot(self):
ppg.util.global_pipegraph.quiet = False
import mbf_sampledata
pasilla_data = pd.read_csv(
mbf_sampledata.get_sample_path(
"mbf_comparisons/pasillaCount_deseq2.tsv.gz"),
sep=" ",
)
# pasilla_data = pasilla_data.set_index('Gene')
pasilla_data.columns = [str(x) for x in pasilla_data.columns]
treated = [x for x in pasilla_data.columns if x.startswith("treated")]
untreated = [
x for x in pasilla_data.columns if x.startswith("untreated")
]
pasilla_data = DelayedDataFrame("pasilla", pasilla_data)
comp = Comparisons(pasilla_data, {
"treated": treated,
"untreated": untreated
}).a_vs_b("treated", "untreated", TTest())
comp.filter([("log2FC", "|>=", 2.0), ("FDR", "<=", 0.05)])
prune_qc(lambda job: "volcano" in job.job_id)
run_pipegraph()
qc_jobs = list(get_qc_jobs())
qc_jobs = [x for x in qc_jobs if not x._pruned]
print(qc_jobs)
assert len(qc_jobs) == 1
assert_image_equal(qc_jobs[0].filenames[0])
def test_edgeR(self):
df = self._get_tuch_data()
ddf = DelayedDataFrame("ex1", df)
gts = {
"T": [x for x in df.columns if ".T" in x],
"N": [x for x in df.columns if ".N" in x],
}
c = Comparisons(ddf, gts)
a = c.a_vs_b("T", "N", EdgeRUnpaired())
force_load(ddf.add_annotator(a))
run_pipegraph()
# these are from the last run - the manual has no simple a vs b comparison...
# at least we'l notice if this changes
assert ddf.df[ddf.df.nameOfGene == "PTHLH"][
a["log2FC"]].values == approx([4.003122])
assert ddf.df[ddf.df.nameOfGene == "PTHLH"][a["FDR"]].values == approx(
[1.332336e-11])
assert ddf.df[ddf.df.nameOfGene == "PTHLH"][a["p"]].values == approx(
[5.066397e-15])
df = ddf.df.set_index("nameOfGene")
t_columns = [x[1] for x in gts["T"]]
n_columns = [x[1] for x in gts["N"]]
assert df.loc["PTHLH"][t_columns].sum(
) > df.loc["PTHLH"][n_columns].sum()
assert ddf.df[ddf.df.nameOfGene == "PTGFR"][
a["log2FC"]].values == approx([-5.127508])
assert ddf.df[ddf.df.nameOfGene == "PTGFR"][a["FDR"]].values == approx(
[6.470885e-10])
assert ddf.df[ddf.df.nameOfGene == "PTGFR"][a["p"]].values == approx(
[3.690970e-13])
assert df.loc["PTGFR"][t_columns].sum(
) < df.loc["PTGFR"][n_columns].sum()
def test_ttest_paired(self):
data = pd.DataFrame({
"A.R1": [0, 0, 0, 0],
"A.R2": [0, 0, 0, 0],
"A.R3": [0, 0.001, 0.001, 0.001],
"B.R1": [0.95, 0, 0.56, 0],
"B.R2": [0.99, 0, 0.56, 0],
"B.R3": [0.98, 0, 0.57, 0.5],
"C.R1": [0.02, 0.73, 0.59, 0],
"C.R2": [0.03, 0.75, 0.57, 0],
"C.R3": [0.05, 0.7, 0.58, 1],
})
ddf = DelayedDataFrame("ex1", data)
gts = {
k: list(v)
for (k,
v) in itertools.groupby(sorted(data.columns), lambda x: x[0])
}
c = Comparisons(ddf, gts)
a = c.a_vs_b("A", "B", TTestPaired())
force_load(ddf.add_annotator(a))
run_pipegraph()
assert ddf.df[a["p"]].iloc[0] == pytest.approx(8.096338300746213e-07,
abs=1e-4)
assert ddf.df[a["p"]].iloc[1] == pytest.approx(0.42264973081037427,
abs=1e-4)
assert ddf.df[a["p"]].iloc[2] == pytest.approx(0.041378369826042816,
abs=1e-4)
assert ddf.df[a["p"]].iloc[3] == pytest.approx(0.42264973081037427,
abs=1e-4)
assert ddf.df[a["FDR"]].values == pytest.approx(
[3.238535e-06, 4.226497e-01, 8.275674e-02, 4.226497e-01], abs=1e-4)
def test_multi_plus_filter(self, clear_annotators):
d = DelayedDataFrame(
"ex1",
pd.DataFrame({
"a1": [1 / 0.99, 2 / 0.99, 3 / 0.99],
"a2": [1 * 0.99, 2 * 0.99, 3 * 0.99],
"b1": [2 * 0.99, 8 * 0.99, (16 * 3) * 0.99],
"b2": [2 / 0.99, 8 / 0.99, (16 * 3) / 0.99],
"delta": [10, 20, 30],
}),
)
c = Comparisons(d, {"a": ["a1", "a2"], "b": ["b1", "b2"]})
a = c.a_vs_b("a", "b", Log2FC(), laplace_offset=0)
anno1 = Constant("shu1", 5)
anno2 = Constant("shu2", 5) # noqa: F841
anno3 = Constant("shu3", 5) # noqa: F841
to_test = [
(("log2FC", "==", -1.0), [-1.0]),
(("log2FC", ">", -2.0), [-1.0]),
(("log2FC", "<", -2.0), [-4.0]),
(("log2FC", ">=", -2.0), [-1.0, -2.0]),
(("log2FC", "<=", -2.0), [-2.0, -4.0]),
(("log2FC", "|>", 2.0), [-4.0]),
(("log2FC", "|<", 2.0), [-1.0]),
(("log2FC", "|>=", 2.0), [-2.0, -4.0]),
(("log2FC", "|<=", 2.0), [-1.0, -2.0]),
((a["log2FC"], "<", -2.0), [-4.0]),
(("log2FC", "|", -2.0), ValueError),
([("log2FC", "|>=", 2.0), ("log2FC", "<=", 0)], [-2.0, -4.0]),
((anno1, ">=", 5), [-1, -2.0, -4.0]),
(((anno1, 0), ">=", 5), [-1, -2.0, -4.0]),
(("shu2", ">=", 5), [-1, -2.0, -4.0]),
(("delta", ">", 10), [-2.0, -4.0]),
]
if not ppg.inside_ppg(): # can't test for missing columns in ppg.
to_test.extend([(("log2FC_no_such_column", "<", -2.0), KeyError)])
filtered = {}
for ii, (f, r) in enumerate(to_test):
if r in (ValueError, KeyError):
with pytest.raises(r):
a.filter([f], "new%i" % ii)
else:
filtered[tuple(f)] = a.filter(
[f] if isinstance(f, tuple) else f, "new%i" % ii)
assert filtered[tuple(f)].name == "new%i" % ii
force_load(filtered[tuple(f)].annotate(),
filtered[tuple(f)].name)
force_load(d.add_annotator(a), "somethingsomethingjob")
run_pipegraph()
c = a["log2FC"]
assert (d.df[c] == [-1.0, -2.0, -4.0]).all()
for f, r in to_test:
if r not in (ValueError, KeyError):
try:
assert filtered[tuple(f)].df[c].values == approx(r)
except AssertionError:
print(f)
raise
def test_deseq2_with_and_without_additional_columns(self):
import mbf_sampledata
pasilla_data = pd.read_csv(
mbf_sampledata.get_sample_path(
"mbf_comparisons/pasillaCount_deseq2.tsv.gz"),
sep=" ",
)
# pasilla_data = pasilla_data.set_index('Gene')
pasilla_data.columns = [str(x) for x in pasilla_data.columns]
print(pasilla_data.columns)
pasilla_data = pasilla_data.assign(
treated_fake=pasilla_data.treated2fb,
untreated_fake=pasilla_data.untreated2fb,
)
gts = {
"treated": [
x for x in pasilla_data.columns
if x.startswith("treated") and "3" not in x
],
"untreated": [
x for x in pasilla_data.columns
if x.startswith("untreated") and "3" not in x
],
"other": [x for x in pasilla_data.columns if "3" in x],
}
assert len(gts["other"]) == 2
assert sum(
(len(x)
for x in gts.values())) + 1 == len(pasilla_data.columns) # GeneId
ddf = DelayedDataFrame("ex", pasilla_data)
c = Comparisons(ddf, gts)
with_other = c.a_vs_b(
"treated",
"untreated",
DESeq2Unpaired(),
include_other_samples_for_variance=True,
)
without_other = c.a_vs_b(
"treated",
"untreated",
DESeq2Unpaired(),
include_other_samples_for_variance=False,
)
force_load(ddf.add_annotator(with_other))
force_load(ddf.add_annotator(without_other))
# run_pipegraph()
df = ddf.df
print(df.head())
df.to_csv("test.csv")
# this is a fairly weak test, but it shows that it at least does *something*
assert (df[with_other["p"]] != pytest.approx(
df[without_other["p"]])).all()
assert (df[with_other["log2FC"]] != pytest.approx(
df[without_other["log2FC"]])).all()
def test_input_checking(self):
d = DelayedDataFrame(
"ex1", pd.DataFrame({
"a": [1, 2, 3],
"b": [2, 8, 16 * 3]
}))
with pytest.raises(ValueError):
Comparisons(None, {})
with pytest.raises(ValueError):
Comparisons(d, {55: {"a"}, "b": ["b"]})
def test_simple(self):
d = DelayedDataFrame(
"ex1", pd.DataFrame({
"a": [1, 2, 3],
"b": [2, 8, 16 * 3]
}))
c = Comparisons(d, {"a": ["a"], "b": ["b"]})
a = c.a_vs_b("a", "b", Log2FC, laplace_offset=0)
assert d.has_annotator(a)
force_load(d.add_annotator(a), "fl1")
run_pipegraph()
assert (d.df[a["log2FC"]] == [-1.0, -2.0, -4.0]).all()
def test_edgeR_filter_on_max_count(self):
ddf, a, b = get_pasilla_data_subset()
gts = {"T": a, "N": b}
c = Comparisons(ddf, gts)
a = c.a_vs_b("T", "N",
EdgeRUnpaired(ignore_if_max_count_less_than=100))
force_load(ddf.add_annotator(a))
run_pipegraph()
assert pd.isnull(ddf.df[a["log2FC"]]).any()
assert (pd.isnull(ddf.df[a["log2FC"]]) == pd.isnull(
ddf.df[a["p"]])).all()
assert (pd.isnull(ddf.df[a["FDR"]]) == pd.isnull(ddf.df[a["p"]])).all()
def test_simple_from_anno_plus_column_pos(self):
d = DelayedDataFrame(
"ex1", pd.DataFrame({
"a": [1, 2, 3],
"b": [2, 8, 16 * 3]
}))
a = Constant("five", 5)
b = Constant("ten", 10)
c = Comparisons(d, {"a": [(a, 0)], "b": [(b, 0)]})
a = c.a_vs_b("a", "b", Log2FC(), laplace_offset=0)
force_load(d.add_annotator(a), "fl1")
run_pipegraph()
assert (d.df[a["log2FC"]] == [-1, -1, -1]).all()
def test_ttest_min_sample_count(self):
df = pd.DataFrame({
"A.R1": [0, 0, 0, 0],
"A.R2": [0, 0, 0, 0],
"B.R1": [0.95, 0, 0.56, 0]
})
ddf = DelayedDataFrame("x", df)
gts = {
k: list(v)
for (k, v) in itertools.groupby(sorted(df.columns), lambda x: x[0])
}
c = Comparisons(ddf, gts)
with pytest.raises(ValueError):
c.a_vs_b("A", "B", TTest())
def test_deseq2(self):
import mbf_sampledata
pasilla_data = pd.read_csv(
mbf_sampledata.get_sample_path(
"mbf_comparisons/pasillaCount_deseq2.tsv.gz"),
sep=" ",
)
# pasilla_data = pasilla_data.set_index('Gene')
pasilla_data.columns = [str(x) for x in pasilla_data.columns]
gts = {
"treated":
[x for x in pasilla_data.columns if x.startswith("treated")],
"untreated":
[x for x in pasilla_data.columns if x.startswith("untreated")],
}
ddf = DelayedDataFrame("ex", pasilla_data)
c = Comparisons(ddf, gts)
a = c.a_vs_b("treated", "untreated", DESeq2Unpaired())
force_load(ddf.add_annotator(a))
run_pipegraph()
check = """# This is deseq2 version specific data- probably needs fixing if upgrading deseq2
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## FBgn0039155 453 -3.72 0.160 -23.2 1.63e-119 1.35e-115
## FBgn0029167 2165 -2.08 0.103 -20.3 1.43e-91 5.91e-88
## FBgn0035085 367 -2.23 0.137 -16.3 6.38e-60 1.75e-56
## FBgn0029896 258 -2.21 0.159 -13.9 5.40e-44 1.11e-40
## FBgn0034736 118 -2.56 0.185 -13.9 7.66e-44 1.26e-40
"""
df = ddf.df.sort_values(a["FDR"])
df = df.set_index("Gene")
for row in check.split("\n"):
row = row.strip()
if row and not row[0] == "#":
row = row.split()
self.assertAlmostEqual(df.ix[row[0]][a["log2FC"]],
float(row[2]),
places=2)
self.assertAlmostEqual(df.ix[row[0]][a["p"]],
float(row[5]),
places=2)
self.assertAlmostEqual(df.ix[row[0]][a["FDR"]],
float(row[6]),
places=2)
def test_double_comparison_with_different_strategies(self):
data = pd.DataFrame({
"A.R1": [0, 0, 0, 0],
"A.R2": [0, 0, 0, 0],
"A.R3": [0, 0.001, 0.001, 0.001],
"B.R1": [0.95, 0, 0.56, 0],
"B.R2": [0.99, 0, 0.56, 0],
"B.R3": [0.98, 0, 0.57, 0.5],
"C.R1": [0.02, 0.73, 0.59, 0],
"C.R2": [0.03, 0.75, 0.57, 0],
"C.R3": [0.05, 0.7, 0.58, 1],
})
ddf = DelayedDataFrame("ex1", data)
gts = {
k: list(v)
for (k,
v) in itertools.groupby(sorted(data.columns), lambda x: x[0])
}
c = Comparisons(ddf, gts)
a = c.a_vs_b("A", "B", TTestPaired())
force_load(ddf.add_annotator(a))
b = c.a_vs_b("A", "B", TTest())
force_load(ddf.add_annotator(b))
run_pipegraph()
assert ddf.df[a["p"]].iloc[0] == pytest.approx(8.096338300746213e-07,
abs=1e-4)
assert ddf.df[a["p"]].iloc[1] == pytest.approx(0.42264973081037427,
abs=1e-4)
assert ddf.df[a["p"]].iloc[2] == pytest.approx(0.041378369826042816,
abs=1e-4)
assert ddf.df[a["p"]].iloc[3] == pytest.approx(0.42264973081037427,
abs=1e-4)
assert ddf.df[a["FDR"]].values == pytest.approx(
[3.238535e-06, 4.226497e-01, 8.275674e-02, 4.226497e-01], abs=1e-4)
assert ddf.df[b["p"]].iloc[0] == pytest.approx(8.096e-07, abs=1e-4)
# value calculated with scipy to double check.
assert ddf.df[b["p"]].iloc[1] == pytest.approx(0.42264973081037427,
abs=1e-4)
assert ddf.df[b["p"]].iloc[2] == pytest.approx(0.04157730613277929,
abs=1e-4)
assert ddf.df[b["p"]].iloc[3] == pytest.approx(0.703158104919873,
abs=1e-4)
assert ddf.df[b["FDR"]].values == pytest.approx(
[3.238535e-06, 5.635329e-01, 8.315462e-02, 7.031581e-01], abs=1e-4)
def test_venn_from_logfcs(self):
ppg.util.global_pipegraph.quiet = False
d = DelayedDataFrame(
"ex1",
pd.DataFrame(
{
"gene_stable_id": ["A", "B", "C", "D", "E"],
"a": [1, 1, 1, 1, 1],
"b": [1, 2, 3, 4, 5],
"c": [1, 1, 3, 0.5, 0.75],
}
),
)
comp = Comparisons(d, {"a": ["a"], "b": ["b"], "c": ["c"]})
a = comp.all_vs_b("a", Log2FC())
selected = {name: x.filter([("log2FC", "|>=", 1)]) for name, x in a.items()}
plot_job = venn.plot_venn("test", selected)
ppg.run_pipegraph()
assert_image_equal(plot_job.filenames[0], "_down")
assert_image_equal(plot_job.filenames[1], "_up")
def test_ma_plot(self):
ppg.util.global_pipegraph.quiet = False
pasilla_data, treated, untreated = get_pasilla_data_subset()
import numpy
numpy.random.seed(500)
comp = Comparisons(pasilla_data, {
"treated": treated,
"untreated": untreated
}).a_vs_b("treated", "untreated", TTest(), laplace_offset=1)
comp.filter([
("log2FC", "|>=", 2.0),
# ('FDR', '<=', 0.05),
])
prune_qc(lambda job: "ma_plot" in job.job_id)
run_pipegraph()
qc_jobs = list(get_qc_jobs())
qc_jobs = [x for x in qc_jobs if not x._pruned]
assert len(qc_jobs) == 1
assert_image_equal(qc_jobs[0].filenames[0])
def test_ttest(self):
data = pd.DataFrame({
"A.R1": [0, 0, 0, 0],
"A.R2": [0, 0, 0, 0],
"A.R3": [0, 0.001, 0.001, 0.001],
"B.R1": [0.95, 0, 0.56, 0],
"B.R2": [0.99, 0, 0.56, 0],
"B.R3": [0.98, 0, 0.57, 0.5],
"C.R1": [0.02, 0.73, 0.59, 0],
"C.R2": [0.03, 0.75, 0.57, 0],
"C.R3": [0.05, 0.7, 0.58, 1],
})
ddf = DelayedDataFrame("ex1", data)
gts = {
k: list(v)
for (k,
v) in itertools.groupby(sorted(data.columns), lambda x: x[0])
}
c = Comparisons(ddf, gts)
a = c.a_vs_b("A", "B", TTest)
b = a.filter([("log2FC", ">", 2.38), ("p", "<", 0.05)])
assert b.name == "Filtered_A-B_log2FC_＞_2.38__p_＜_0.05"
force_load(ddf.add_annotator(a))
run_pipegraph()
# value calculated with R to double check.
assert ddf.df[a["p"]].iloc[0] == pytest.approx(8.096e-07, abs=1e-4)
# value calculated with scipy to double check.
assert ddf.df[a["p"]].iloc[1] == pytest.approx(0.42264973081037427,
abs=1e-4)
assert ddf.df[a["p"]].iloc[2] == pytest.approx(0.04157730613277929,
abs=1e-4)
assert ddf.df[a["p"]].iloc[3] == pytest.approx(0.703158104919873,
abs=1e-4)
assert ddf.df[a["FDR"]].values == pytest.approx(
[3.238535e-06, 5.635329e-01, 8.315462e-02, 7.031581e-01], abs=1e-4)
def test_correlation(self):
ppg.util.global_pipegraph.quiet = False
import mbf_sampledata
pasilla_data = pd.read_csv(
mbf_sampledata.get_sample_path(
"mbf_comparisons/pasillaCount_deseq2.tsv.gz"),
sep=" ",
)
# pasilla_data = pasilla_data.set_index('Gene')
pasilla_data.columns = [str(x) for x in pasilla_data.columns]
treated = [x for x in pasilla_data.columns if x.startswith("treated")]
untreated = [
x for x in pasilla_data.columns if x.startswith("untreated")
]
pasilla_data = DelayedDataFrame("pasilla", pasilla_data)
Comparisons(pasilla_data, {"treated": treated, "untreated": untreated})
prune_qc(lambda job: "correlation" in job.job_id)
run_pipegraph()
qc_jobs = list(get_qc_jobs())
qc_jobs = [x for x in qc_jobs if not x._pruned]
print(qc_jobs)
assert len(qc_jobs) == 1
assert_image_equal(qc_jobs[0].filenames[0])