Skip to content

Commit

Permalink
modified top ranking table creation to use postprocessing methods and…
Browse files Browse the repository at this point in the history 
… to allow for creation of top ranking CO tables
  • Loading branch information
@ashuaibi7
ashuaibi7 committed Jan 16, 2025
1 parent 9bf02b5 commit b51fd42
Showing 1 changed file with 59 additions and 97 deletions.
156 changes: 59 additions & 97 deletions analysis/top_ranking_pairs_tex_table.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,9 @@
import logging
import pandas as pd
import numpy as np
from argparse import ArgumentParser

EPSILON_MUTATION_COUNT = 10
PVALUE_THRESHOLD = 1
from argparse import ArgumentParser
from dialect.utils.postprocessing import generate_top_ranking_tables


# ---------------------------------------------------------------------------- #
Expand All @@ -15,13 +14,13 @@ def build_argument_parser():
"""
We do NOT modify this parser, as requested.
"""
parser = ArgumentParser(description="Generate LaTeX tables for top ME pairs across methods.")
parser = ArgumentParser(description="Generate LaTeX tables for top pairs across methods.")
parser.add_argument(
"-k",
"--top_k",
"-n",
"--num_pairs",
type=int,
default=10,
help="Number of top ranking pairs to visualize",
help="Number of top ranking pairs to include in table",
)
parser.add_argument(
"-r",
Expand All @@ -34,23 +33,34 @@ def build_argument_parser():
"-dvr",
"--driver_genes_fn",
type=str,
required=True,
default="data/references/OncoKB_Cancer_Gene_List.tsv",
help="File with driver genes",
)
parser.add_argument(
"-d",
"--decoy_genes_dir",
type=str,
required=True,
default="data/decoy_genes",
help="Directory with all decoy gene files",
)
parser.add_argument(
"-o",
"--out",
type=str,
required=True,
default="tables",
help="Output directory for tex files",
)
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument(
"--me",
action="store_true",
help="Perform analysis for mutual exclusivity",
)
group.add_argument(
"--co",
action="store_true",
help="Perform analysis for co-occurrence",
)
return parser


Expand Down Expand Up @@ -94,7 +104,7 @@ def escape_gene_name(gene_name):
return gene_name.replace("_M", r"\_M").replace("_N", r"\_N")


def build_subtable_latex(methods_list, top_pairs_by_method, metric_labels):
def build_subtable_latex(methods_list, top_pairs_by_method, metric_labels, is_me):
"""
Builds a LaTeX fragment for the given set of methods in a single row of columns.
E.g., ["DIALECT","DISCOVER","Fisher's Exact Test"] -> a 3-method tabular.
Expand All @@ -103,7 +113,7 @@ def build_subtable_latex(methods_list, top_pairs_by_method, metric_labels):
col_spec = "||".join(["cc"] * num_methods)

lines = []
lines.append(r"\renewcommand{\arraystretch}{1.2}") # Slightly bigger spacing
lines.append(r"\renewcommand{\arraystretch}{1.2}")
lines.append(r"\begin{tabular}{" + col_spec + r"}")
lines.append(r"\hline")

Expand All @@ -114,7 +124,8 @@ def build_subtable_latex(methods_list, top_pairs_by_method, metric_labels):

subheader_parts = []
for method in methods_list:
subheader_parts.append("ME Gene Pair")
col_name = "ME Gene Pair" if is_me else "CO Gene Pair"
subheader_parts.append(col_name)
subheader_parts.append(metric_labels[method])
lines.append(" & ".join(subheader_parts) + r" \\ \hline")

Expand All @@ -140,7 +151,7 @@ def build_subtable_latex(methods_list, top_pairs_by_method, metric_labels):
# ---------------------------------------------------------------------------- #
# MAIN FUNCTIONS #
# ---------------------------------------------------------------------------- #
def create_final_table(subtype, top_pairs_by_method, top_k):
def create_final_table(subtype, top_pairs_by_method, num_pairs, is_me):
"""
Creates one big table environment with two "sub-tables":
- First row (3 methods): DIALECT, DISCOVER, Fisher's Exact Test
Expand All @@ -153,26 +164,30 @@ def create_final_table(subtype, top_pairs_by_method, top_k):
"Fisher's Exact Test": "p-value",
"MEGSA": "S-Score",
"WeSME": "p-value",
"WeSCO": "p-value",
}

top_row_methods = ["DIALECT", "DISCOVER", "Fisher's Exact Test"]
bottom_row_methods = ["MEGSA", "WeSME"]
bottom_row_methods = ["MEGSA"]
if is_me:
bottom_row_methods.append("WeSME")
else:
bottom_row_methods.append("WeSCO")

top_subtable = build_subtable_latex(top_row_methods, top_pairs_by_method, metric_labels)
bottom_subtable = build_subtable_latex(bottom_row_methods, top_pairs_by_method, metric_labels)
top_subtable = build_subtable_latex(top_row_methods, top_pairs_by_method, metric_labels, is_me)
bottom_subtable = build_subtable_latex(
bottom_row_methods, top_pairs_by_method, metric_labels, is_me
)

lines = []
lines.append(r"\begin{table}[htbp]")
lines.append(r"\centering")

# Top sub-table (DIALECT, DISCOVER, FET)
lines.append(top_subtable)
# Tiny vertical gap
lines.append(r"\vspace{-0.2cm}")
# Bottom sub-table (MEGSA, WeSME)
lines.append(bottom_subtable)

lines.append(rf"\caption{{Top {top_k} ranked ME pairs across methods in {subtype}}}")
lines.append(rf"\caption{{Top {num_pairs} ranked ME pairs across methods in {subtype}}}")
lines.append(r"\label{tab:" + subtype + "}")
lines.append(r"\end{table}")

Expand All @@ -185,99 +200,46 @@ def create_final_table(subtype, top_pairs_by_method, top_k):

os.makedirs(args.out, exist_ok=True)

methods_info = {
"DIALECT": {
"column": "Rho",
"ascending": True,
},
"DISCOVER": {
"column": "Discover ME P-Val",
"ascending": True,
},
"Fisher's Exact Test": {
"column": "Fisher's ME P-Val",
"ascending": True,
},
"MEGSA": {
"column": "MEGSA S-Score (LRT)",
"ascending": False,
},
"WeSME": {
"column": "WeSME P-Val",
"ascending": True,
},
}

subtypes = os.listdir(args.results_dir)
for subtype in subtypes:
results_fn = os.path.join(args.results_dir, subtype, "complete_pairwise_ixn_results.csv")
cnt_mtx_fn = os.path.join(args.results_dir, subtype, "count_matrix.csv")
num_samples = pd.read_csv(cnt_mtx_fn, index_col=0).shape[0]
if not os.path.exists(results_fn):
if not os.path.exists(results_fn) or not os.path.exists(cnt_mtx_fn):
logging.info(f"Skipping {subtype}: file not found.")
continue
num_samples = pd.read_csv(cnt_mtx_fn, index_col=0).shape[0]
results_df = pd.read_csv(results_fn)

top_tables = generate_top_ranking_tables(
results_df=results_df,
is_me=args.me,
num_pairs=args.num_pairs,
num_samples=num_samples,
)
top_pairs_by_method = {}
for method_name, info in methods_info.items():
col_name = info["column"]
ascending = info["ascending"]

if col_name not in results_df.columns:
logging.warning(
f"Column {col_name} not found in {results_fn} for {subtype}. Skipping {method_name}."
)
for method_name, method_df in top_tables.items():
if method_df is None or method_df.empty:
logging.info(f"No top pairs for method: {method_name}")
top_pairs_by_method[method_name] = []
continue

# 1) Subset as per the method's rules
method_df = results_df.copy()

if method_name == "DIALECT":
epsilon = EPSILON_MUTATION_COUNT / num_samples
method_df = method_df[method_df["Rho"] < 0]
method_df = method_df[
(method_df["Tau_1X"] > epsilon) & (method_df["Tau_X1"] > epsilon)
]

if method_name == "MEGSA":
method_df = method_df[method_df["MEGSA S-Score (LRT)"] > 0]

if method_name == "DISCOVER":
method_df = method_df[method_df["Discover ME P-Val"] < PVALUE_THRESHOLD]

if method_name == "Fisher's Exact Test":
method_df = method_df[method_df["Fisher's ME P-Val"] < PVALUE_THRESHOLD]

if method_name == "WeSME":
method_df = method_df[method_df["WeSME P-Val"] < PVALUE_THRESHOLD]

# 2) Sort by the column, then pick top K
if not method_df.empty:
method_df = method_df.sort_values(col_name, ascending=ascending).head(args.top_k)
else:
top_pairs_by_method[method_name] = []
continue

# 3) Construct the final list of (ME Gene Pair, value_str)
pairs_list = []
metric_col_name = method_df.columns[-1]
for _, row in method_df.iterrows():
geneA = escape_gene_name(str(row["Gene A"]))
geneB = escape_gene_name(str(row["Gene B"]))

metric_val = row[metric_col_name]
val_str = format_float(metric_val) if metric_val is not None else "N/A"
interaction_str = f"{geneA}:{geneB}"
val = row[col_name]
val_str = format_float(val)
pairs_list.append((interaction_str, val_str))

if method_name == "WeSME" and args.co:
method_name = "WeSCO"
top_pairs_by_method[method_name] = pairs_list

# Build the final LaTeX table
latex_str = create_final_table(subtype, top_pairs_by_method, args.top_k)

# Save to file
out_filename = os.path.join(args.out, f"table_of_top_pairs_{subtype}.tex")
with open(out_filename, "w") as f:
latex_str = create_final_table(subtype, top_pairs_by_method, args.num_pairs, args.me)
if args.me:
fout = os.path.join(args.out, f"table_of_top_me_pairs_{subtype}.tex")
else:
fout = os.path.join(args.out, f"table_of_top_co_pairs_{subtype}.tex")
with open(fout, "w") as f:
f.write(latex_str)

logging.info(f"Wrote LaTeX table for {subtype} to {out_filename}")
logging.info(f"Wrote LaTeX table for {subtype} to {fout}")

0 comments on commit b51fd42

Please sign in to comment.