Parameters for Python wrapper of R function

Author: zmzhang

python/LCMSSimulation.py

@@ -174,7 +174,7 @@ def match_features(ground_truths, df):
 
  from r_functions import XCMS
  tic()
- df_xcms = XCMS(mzMLfile)
+ df_xcms = XCMS(mzMLfile, w1=5, w2=12, snr=3, intensity=10)
  toc()
  match_xcms = ground_truths.copy()
  match_features(match_xcms, df_xcms)

python/r_functions.py

@@ -24,10 +24,10 @@ def init_r():
  XC = robjects.globalenv['XC']
  return PIT, XC
 
-def XCMS(mzMLFile):
+def XCMS(mzMLFile, w1, w2, snr, intensity):
  df = pd.DataFrame(columns=['rt', 'mz', 'intensity'])
  _,XC = init_r()
- peaks_xcms = np.array(XC(mzXMLFile=mzMLFile))
+ peaks_xcms = np.array(XC(mzXMLFile=mzMLFile, w1=w1, w2=w2, snr=snr, intensity=intensity))
  for i in range(peaks_xcms.shape[0]):
  rt = peaks_xcms[i,3]
  mz = peaks_xcms[i,0]