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Merged
abearab merged 3 commits into from
Dec 17, 2024
Merged

Improve dashboard scripts #99

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3cf220a
update data preparation and improve variable handling
abearab Dec 16, 2024
86aa18c
update `_prep_data` and auto run in `__init__`
abearab Dec 16, 2024
614556e
update workflows to use setup-miniconda@v3
abearab Dec 17, 2024
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3 changes: 1 addition & 2 deletions .github/workflows/python-package.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,10 @@ jobs:
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: "Install miniconda"
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: "latest"
auto-update-conda: true
mamba-version: "*"
python-version: ${{ matrix.python-version }}
channels: conda-forge,bioconda
environment-file: environment.yml
Expand Down
3 changes: 1 addition & 2 deletions .github/workflows/python-publish.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,10 @@ jobs:
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: "Install miniconda"
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: "latest"
auto-update-conda: true
mamba-version: "*"
python-version: ${{ matrix.python-version }}
channels: conda-forge,bioconda
environment-file: environment.yml
Expand Down
34 changes: 16 additions & 18 deletions screenpro/dashboard/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,30 +38,36 @@ def _get_html(self, p):

class DrugScreenDashboard(DataDashboard):

def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label='negative_control',run_name='auto'):
def __init__(
self, screen, treated, untreated,
t0='T0', threshold=3, ctrl_label='negative_control',
run_name='auto',
score_col='score', pvalue_col='pvalue'
):
self.screen = screen
self.threshold = threshold
self.ctrl_label = ctrl_label
self.run_name = run_name
self.gamma_score_name = f'gamma:{untreated}_vs_{t0}'
self.rho_score_name = f'rho:{treated}_vs_{untreated}'
self.df = self._prep_data(screen, score_col=score_col, pvalue_col=pvalue_col)
self.plots = {}
super().__init__()

def _prep_data(self,screen, score_col='score', pvalue_col='pvalue'):

gamma = screen.getPhenotypeScores(
phenotype_name=self.gamma_score_name,
run_name=self.run_name,
score_name=self.gamma_score_name,
threshold=self.threshold,
ctrl_label=self.ctrl_label,
score_col=score_col,
pvalue_col=pvalue_col
)

rho = screen.getPhenotypeScores(
phenotype_name=self.rho_score_name,
run_name=self.run_name,
score_name=self.rho_score_name,
threshold=self.threshold,
ctrl_label=self.ctrl_label,
score_col=score_col,
Expand All @@ -71,17 +77,17 @@ def _prep_data(self,screen, score_col='score', pvalue_col='pvalue'):
df = pd.DataFrame({
'target': rho['target'],
'rho_score': rho['score'],
'rho_pvalue': rho['pvalue'],
'rho_pvalue': rho[pvalue_col],
'rho_label': rho['label'],
'-log10(rho_pvalue)': np.log10(rho['pvalue']) * -1,
'-log10(rho_pvalue)': np.log10(rho[pvalue_col]) * -1,
'gamma_score': gamma.loc[rho.index,'score'],
'gamma_pvalue': gamma.loc[rho.index,'pvalue'],
'gamma_pvalue': gamma.loc[rho.index,pvalue_col],
'gamma_label': gamma.loc[rho.index,'label'],
'-log10(gamma_pvalue)': np.log10(gamma.loc[rho.index,'pvalue']) * -1,
'-log10(gamma_pvalue)': np.log10(gamma.loc[rho.index,pvalue_col]) * -1,
})

return df

def _plot_scatter(
self,
x_source,y_source,
Expand All @@ -93,11 +99,9 @@ def _plot_scatter(
dot_size=1,
width=500, height=400,
toolbar_location='below',
legend_loc="top_left"
legend_loc="top_left",
):

df = self._prep_data(self.screen)

df = self.df.copy()
if y_max == 'auto': y_max = df[y_source].max() * 1.2
if x_max == 'auto': x_max = df[x_source].max() * 1.2
if y_min == 'auto': y_min = df[y_source].min() * 1.2
Expand Down Expand Up @@ -216,15 +220,13 @@ def RhoVolcanoPlot(
hit_label_col='rho_label',
x_min=-2.5, x_max=2.5, y_min=0, y_max='auto',
return_html=True,
**kwargs
):
p = self._plot_scatter(
x_source, y_source,
xaxis_label, yaxis_label,
up_hit, down_hit,
hit_label_col,
x_min, x_max, y_min, y_max,
**kwargs
)

if return_html:
Expand All @@ -243,15 +245,13 @@ def GammaVolcanoPlot(
hit_label_col='gamma_label',
x_min=-2.5, x_max=2.5, y_min=0, y_max='auto',
return_html=True,
**kwargs
):
p = self._plot_scatter(
x_source, y_source,
xaxis_label, yaxis_label,
up_hit, down_hit,
hit_label_col,
x_min, x_max, y_min, y_max,
**kwargs
)

if return_html:
Expand All @@ -270,15 +270,13 @@ def RhoGammaScatter(
hit_label_col='rho_label',
return_html=True,
x_min=-2.5, x_max=2.5, y_min=-2.5, y_max=2.5,
**kwargs
):
p = self._plot_scatter(
x_source, y_source,
xaxis_label, yaxis_label,
up_hit, down_hit,
hit_label_col,
x_min, x_max, y_min, y_max,
**kwargs
)

if return_html:
Expand Down
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