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Copy pathrun_marker_function.py
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366 lines (310 loc) · 11.4 KB
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"""Flexible wrapper to call any markeR R function from Python.
This script allows you to call markeR functions directly without writing Python code.
Usage examples:
python run_marker_function.py PlotScores --help-function
python run_marker_function.py CalculateScores \\
--data counts_example --metadata metadata_example \\
--gene_sets genesets_example --method logmedian --verbose
python run_marker_function.py PlotScores \\
--data counts_example --metadata metadata_example \\
--gene_sets genesets_example --Variable "Condition" \\
--method logmedian --nrow 1 --output plot.png
Options:
--help-function Show R documentation for the function
--verbose Print the generated R code before executing
--output FILE Save plot to PNG file
For built-in example data, use the names: counts_example, metadata_example, genesets_example
"""
import sys
import argparse
import json
import os
import re
# Check dependencies
_missing = []
try:
import rpy2.robjects as ro
from rpy2.robjects.packages import importr, isinstalled
except ImportError:
_missing.append("rpy2")
if _missing:
sys.exit(
"The following Python packages are required but not installed: %s.\n"
"Please install them (e.g. `pip install rpy2`)." % ", ".join(_missing)
)
def ensure_bioc_installed() -> None:
"""Install Bioconductor's package manager if it is not already present."""
biocinstaller = "BiocManager"
if not isinstalled(biocinstaller):
ro.r('install.packages("{0}")'.format(biocinstaller))
ro.r('suppressMessages(require({0}))'.format(biocinstaller))
def install_markeR() -> None:
"""Install the markeR package from Bioconductor if not already installed."""
ensure_bioc_installed()
if not isinstalled("markeR"):
ro.r('BiocManager::install("markeR", ask=FALSE, update=FALSE)')
ro.r('library(markeR)')
def load_example_data():
"""Load built-in markeR example datasets into R namespace."""
install_markeR()
# Load the example datasets
ro.r('data("genesets_example", package="markeR")')
ro.r('data("counts_example", package="markeR")')
ro.r('data("metadata_example", package="markeR")')
print("Loaded markeR example datasets: counts_example, metadata_example, genesets_example")
def parse_parameter(value: str):
"""
Parse a parameter value intelligently.
- Numbers become numeric
- "true"/"false" become logical
- "null" becomes NULL
- R object names (e.g., counts_example) are kept as-is
- JSON objects/arrays become R equivalents
- Strings are kept as strings
"""
value_lower = value.lower()
# Handle boolean
if value_lower == "true":
return "TRUE"
if value_lower == "false":
return "FALSE"
if value_lower == "null":
return "NULL"
# Handle numbers
try:
if "." in value:
float(value)
return value
else:
int(value)
return value
except ValueError:
pass
# Check if it's a known R object name (example data)
known_objects = ["counts_example", "metadata_example", "genesets_example"]
if value in known_objects:
return value
# Try JSON parsing for objects/arrays
try:
json.loads(value)
# If it parses as JSON, return as-is (user can provide lists as JSON)
return value
except (json.JSONDecodeError, ValueError):
pass
# Default: treat as string, escaping any internal quotes
value = value.replace('"', '\\"')
return f'"{value}"'
def build_r_call(function_name: str, params: dict, output_file: str = None, width: int = 800, height: int = 600) -> str:
"""
Build an R function call string from parameters.
Parameters
----------
function_name : str
Name of the R function to call
params : dict
Dictionary of parameter names and values
output_file : str
If provided, set up PNG device before the call and close after
width : int
PNG width in pixels (default: 800)
height : int
PNG height in pixels (default: 600)
Returns
-------
str
Complete R code to execute
"""
# Remove output_file from params if present
params = {k: v for k, v in params.items() if k != "output_file"}
# Build parameter list
param_strings = []
for key, value in params.items():
parsed_value = parse_parameter(value)
param_strings.append(f"{key} = {parsed_value}")
param_str = ", ".join(param_strings)
# Build R code
r_code = ""
if output_file:
output_file = os.path.abspath(output_file)
dirname = os.path.dirname(output_file)
if dirname and not os.path.isdir(dirname):
os.makedirs(dirname, exist_ok=True)
r_code += f'png("{output_file}", width={width}, height={height})\n'
r_code += f"result <- {function_name}({param_str})\n"
r_code += "tryCatch(print(result), error=function(e) { invisible(NULL) })\n"
r_code += "dev.off()\n"
else:
# For screen output, try to print the result
r_code += f"result <- {function_name}({param_str})\n"
r_code += "tryCatch(print(result), error=function(e) { cat('Function executed.\\n') })\n"
return r_code
def main():
parser = argparse.ArgumentParser(
description="Call any markeR R function from Python",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
Examples:
python run_marker_function.py CalculateScores \\
--data counts_example --metadata metadata_example \\
--gene_sets genesets_example --method logmedian
python run_marker_function.py PlotScores \\
--data counts_example --metadata metadata_example \\
--gene_sets genesets_example --Variable "Condition" \\
--method logmedian --output my_plot.png
Built-in example data: counts_example, metadata_example, genesets_example
"""
)
parser.add_argument(
"function_name",
help="Name of the markeR function to call (e.g., CalculateScores, PlotScores)"
)
parser.add_argument(
"--help-function",
action="store_true",
help="Show help for the R function (instead of calling it)"
)
parser.add_argument(
"--verbose",
action="store_true",
help="Print the generated R code before executing"
)
parser.add_argument(
"--output",
help="Save plot output to a PNG file"
)
parser.add_argument(
"--width",
type=int,
default=800,
help="PNG width in pixels (default: 800)"
)
parser.add_argument(
"--height",
type=int,
default=600,
help="PNG height in pixels (default: 600)"
)
# Allow arbitrary parameters
parser.add_argument(
"params",
nargs="*",
help="Parameters as --name value pairs (e.g., --data counts_example --method logmedian)"
)
# Handle --help for specific functions
if len(sys.argv) > 1 and sys.argv[1] not in ["--help", "-h"]:
if "--help-function" in sys.argv:
func_name = sys.argv[1]
print(f"\n{'='*70}")
print(f"Help for markeR::{func_name}")
print(f"{'='*70}\n")
install_markeR()
# Try to display help
try:
# Get function signature and description
ro.r(f'''
library(markeR)
cat("Function: {func_name}\\n\\n")
# Try to get help
tryCatch({{
help_file <- help("{func_name}", package="markeR")
# Get description from help
}}, error = function(e) {{
cat("Help available at: https://diseasetranscriptomicslab.github.io/markeR/reference/{func_name}.html\\n")
}})
''')
except Exception as e:
pass
print(f"\nDocumentation:")
print(f" https://diseasetranscriptomicslab.github.io/markeR/reference/{func_name}.html")
print(f"\nTo use this function:")
print(f" python run_marker_function.py {func_name} --param1 value1 --param2 value2 [--output output.png]")
print(f"\nTip: Use --verbose flag to see generated R code")
print(f" python run_marker_function.py {func_name} --verbose --param1 value1 ...\n")
print(f"{'='*70}\n")
return
# Parse args
if len(sys.argv) < 2:
parser.print_help()
return
func_name = sys.argv[1]
# Validate function name to prevent code injection
if not re.match(r'^[A-Za-z][A-Za-z0-9_.]*$', func_name):
sys.exit(f"Error: invalid function name '{func_name}'. "
"Function names must start with a letter and contain only letters, digits, dots or underscores.")
output_file = None
width = 800
height = 600
# Parse remaining arguments as key-value pairs
params = {}
i = 2
while i < len(sys.argv):
arg = sys.argv[i]
if arg == "--output" and i + 1 < len(sys.argv):
output_file = sys.argv[i + 1]
i += 2
elif arg == "--width" and i + 1 < len(sys.argv):
try:
width = int(sys.argv[i + 1])
except ValueError:
print(f"Error: --width must be a number, got '{sys.argv[i + 1]}'")
sys.exit(1)
i += 2
elif arg == "--height" and i + 1 < len(sys.argv):
try:
height = int(sys.argv[i + 1])
except ValueError:
print(f"Error: --height must be a number, got '{sys.argv[i + 1]}'")
sys.exit(1)
i += 2
elif arg in ["--verbose", "--help-function"]:
# Skip flags that are not parameters
i += 1
elif arg.startswith("--"):
key = arg[2:] # Remove --
if i + 1 < len(sys.argv) and not sys.argv[i + 1].startswith("--"):
value = sys.argv[i + 1]
params[key] = value
i += 2
else:
# Boolean flag
params[key] = "TRUE"
i += 1
else:
i += 1
# Ensure markeR is installed
print("Installing markeR if needed...")
install_markeR()
load_example_data()
# Build and execute the R call
print(f"\nCalling {func_name} with parameters:")
for key, value in params.items():
print(f" {key} = {value}")
if output_file:
print(f" Saving plot to: {output_file}")
print(f" PNG dimensions: {width}x{height} pixels")
r_code = build_r_call(func_name, params, output_file, width, height)
# Show R code if verbose mode
if "--verbose" in sys.argv:
print(f"\n{'='*70}")
print("Generated R code:")
print(f"{'='*70}")
print(r_code)
print(f"{'='*70}\n")
print(f"Executing R code...\n")
print("=" * 60)
try:
ro.r(r_code)
print("=" * 60)
if output_file:
print(f"\n✓ Plot saved to: {output_file}")
else:
print(f"\n✓ Function executed successfully")
except Exception as e:
print("=" * 60)
print(f"\n✗ Error executing function: {e}")
if "--verbose" not in sys.argv:
print("\nTip: Use --verbose flag to see the generated R code")
print(f" python run_marker_function.py {func_name} --verbose [other options]")
sys.exit(1)
if __name__ == "__main__":
main()
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