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Updated controls to both Irida and PCR.

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This commit is contained in:
lwark
2024-10-16 15:07:43 -05:00
parent 066d1af0f2
commit c3a4aac68b
11 changed files with 750 additions and 314 deletions
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50
src/submissions/frontend/visualizations/__init__.py
View File

@@ -1,4 +1,52 @@
'''
Contains all operations for creating charts, graphs and visual effects.
'''
from .control_charts import *
from PyQt6.QtWidgets import QWidget
import plotly
from plotly.graph_objects import Figure
import pandas as pd
from frontend.widgets.functions import select_save_file
class CustomFigure(Figure):
def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
months: int = 6):
super().__init__()
def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
"""
Writes plotly figure to html file.
Args:
figs ():
settings (dict): settings passed down from click
fig (Figure): input figure object
group_name (str): controltype
"""
output = select_save_file(obj=parent, default_name=group_name, extension="png")
self.write_image(output.absolute().__str__(), engine="kaleido")
def to_html(self) -> str:
"""
Creates final html code from plotly
Args:
figure (Figure): input figure
Returns:
str: html string
"""
html = '<html><body>'
if self is not None:
html += plotly.offline.plot(self, output_type='div',
include_plotlyjs='cdn') #, image = 'png', auto_open=True, image_filename='plot_image')
else:
html += "<h1>No data was retrieved for the given parameters.</h1>"
html += '</body></html>'
return html
from .irida_charts import IridaFigure
from .pcr_charts import PCRFigure

58
src/submissions/frontend/visualizations/control_charts.py → src/submissions/frontend/visualizations/irida_charts.py
View File

@@ -1,15 +1,13 @@
"""
Functions for constructing controls graphs using plotly.
Functions for constructing irida controls graphs using plotly.
"""
from copy import deepcopy
from datetime import date
from pprint import pformat
import plotly
import plotly.express as px
import pandas as pd
from PyQt6.QtWidgets import QWidget
from plotly.graph_objects import Figure
from . import CustomFigure
import logging
from tools import get_unique_values_in_df_column, divide_chunks
from frontend.widgets.functions import select_save_file
@@ -17,11 +15,12 @@ from frontend.widgets.functions import select_save_file
logger = logging.getLogger(f"submissions.{__name__}")
class CustomFigure(Figure):
class IridaFigure(CustomFigure):
def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
months: int = 6):
super().__init__()
super().__init__(df=df, modes=modes)
self.construct_chart(df=df, modes=modes)
self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
@@ -105,25 +104,16 @@ class CustomFigure(Figure):
self.update_xaxes(
rangeslider_visible=True,
rangeselector=dict(
# buttons=list([
# dict(count=1, label="1m", step="month", stepmode="backward"),
# dict(count=3, label="3m", step="month", stepmode="backward"),
# dict(count=6, label="6m", step="month", stepmode="backward"),
# dict(count=1, label="YTD", step="year", stepmode="todate"),
# dict(count=12, label="1y", step="month", stepmode="backward"),
# dict(step="all")
# ])
buttons=[button for button in self.make_plotly_buttons(months=months)]
)
)
assert isinstance(self, Figure)
# return fig
assert isinstance(self, CustomFigure)
def make_plotly_buttons(self, months:int=6):
def make_plotly_buttons(self, months: int = 6):
rng = [1]
if months > 2:
rng += [iii for iii in range(3, months, 3)]
logger.debug(f"Making buttons for months: {rng}")
# logger.debug(f"Making buttons for months: {rng}")
buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
if months > date.today().month:
buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
@@ -161,35 +151,3 @@ class CustomFigure(Figure):
{"yaxis.title.text": mode},
])
def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
"""
Writes plotly figure to html file.
Args:
figs ():
settings (dict): settings passed down from click
fig (Figure): input figure object
group_name (str): controltype
"""
output = select_save_file(obj=parent, default_name=group_name, extension="png")
self.write_image(output.absolute().__str__(), engine="kaleido")
def to_html(self) -> str:
"""
Creates final html code from plotly
Args:
figure (Figure): input figure
Returns:
str: html string
"""
html = '<html><body>'
if self is not None:
html += plotly.offline.plot(self, output_type='div',
include_plotlyjs='cdn') #, image = 'png', auto_open=True, image_filename='plot_image')
else:
html += "<h1>No data was retrieved for the given parameters.</h1>"
html += '</body></html>'
return html

34
src/submissions/frontend/visualizations/pcr_charts.py Normal file
View File

@@ -0,0 +1,34 @@
"""
Functions for constructing irida controls graphs using plotly.
"""
from datetime import date
from pprint import pformat
import plotly
from . import CustomFigure
import plotly.express as px
import pandas as pd
from PyQt6.QtWidgets import QWidget
from plotly.graph_objects import Figure
import logging
from tools import get_unique_values_in_df_column, divide_chunks
from frontend.widgets.functions import select_save_file
logger = logging.getLogger(f"submissions.{__name__}")
class PCRFigure(CustomFigure):
def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
months: int = 6):
super().__init__(df=df, modes=modes)
self.construct_chart(df=df)
# self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
def construct_chart(self, df: pd.DataFrame):
logger.debug(f"PCR df: {df}")
try:
scatter = px.scatter(data_frame=df, x='submitted_date', y="ct", hover_data=["name", "target", "ct", "reagent_lot"], color='target')
except ValueError:
scatter = px.scatter()
self.add_traces(scatter.data)