import os
from typing import Any, cast
from duckdb import DuckDBPyConnection
import polars as pl
import altair as alt
from ecoli.library.parquet_emitter import num_cells, read_stacked_columns
COLORS_256 = [ # From colorbrewer2.org, qualitative 8-class set 1
[228, 26, 28],
[55, 126, 184],
[77, 175, 74],
[152, 78, 163],
[255, 127, 0],
[255, 255, 51],
[166, 86, 40],
[247, 129, 191],
]
COLORS = ["#%02x%02x%02x" % (color[0], color[1], color[2]) for color in COLORS_256]
[docs]
def plot(
params: dict[str, Any],
conn: DuckDBPyConnection,
history_sql: str,
config_sql: str,
success_sql: str,
sim_data_paths: dict[str, dict[int, str]],
validation_data_paths: list[str],
outdir: str,
variant_metadata: dict[str, dict[int, Any]],
variant_names: dict[str, str],
):
assert num_cells(conn, config_sql) == 1, (
"Mass fraction summary plot requires single-cell data."
)
mass_columns = {
"Protein": "listeners__mass__protein_mass",
"tRNA": "listeners__mass__tRna_mass",
"rRNA": "listeners__mass__rRna_mass",
"mRNA": "listeners__mass__mRna_mass",
"DNA": "listeners__mass__dna_mass",
"Small Mol": "listeners__mass__smallMolecule_mass",
"Dry": "listeners__mass__dry_mass",
}
mass_data = pl.DataFrame(
read_stacked_columns(history_sql, list(mass_columns.values()), conn=conn)
)
fractions = {
k: cast(float, (mass_data[v] / mass_data["listeners__mass__dry_mass"]).mean())
for k, v in mass_columns.items()
}
new_columns = {
"Time (min)": (mass_data["time"] - mass_data["time"].min()) / 60,
**{
f"{k} ({fractions[k]:.3f})": mass_data[v] / mass_data[v][0]
for k, v in mass_columns.items()
},
}
mass_fold_change_df = pl.DataFrame(new_columns)
# Altair requires long form data (also no periods in column names)
melted_df = mass_fold_change_df.melt(
id_vars="Time (min)",
variable_name="Submass",
value_name="Mass (normalized by t = 0 min)",
)
chart = (
alt.Chart(melted_df)
.mark_line()
.encode(
x=alt.X("Time (min):Q", title="Time (min)"),
y=alt.Y("Mass (normalized by t = 0 min):Q"),
color=alt.Color("Submass:N", scale=alt.Scale(range=COLORS)),
)
.properties(
title="Biomass components (average fraction of total dry mass in parentheses)"
)
)
chart.save(os.path.join(outdir, "mass_fraction_summary.html"))