masster 0.3.2__py3-none-any.whl → 0.3.4__py3-none-any.whl

masster/sample/sample.py

@@ -202,9 +202,9 @@ class Sample:
     find_adducts = find_adducts
     find_ms2 = find_ms2
     get_spectrum = get_spectrum
-    filter = filter
+    filter = features_filter
     select = select
-    features_filter = features_filter  # New function that keeps only specified features
+    features_filter = filter  # New function that keeps only specified features
     filter_features = filter
     features_select = select
     select_features = select

masster/study/plot.py

@@ -161,7 +161,9 @@ def plot_consensus_2d(
     alpha=0.7,
     cmap=None,
     width=900,
-    height=900
+    height=900,
+    mz_range=None,
+    rt_range=None
 ):
     """
     Plot consensus features in a 2D scatter plot with retention time vs m/z.
@@ -178,11 +180,20 @@ def plot_consensus_2d(
         cmap (str, optional): Color map name
         width (int): Plot width in pixels (default: 900)
         height (int): Plot height in pixels (default: 900)
+        mz_range (tuple, optional): m/z range for filtering consensus features (min_mz, max_mz)
+        rt_range (tuple, optional): Retention time range for filtering consensus features (min_rt, max_rt)
     """
     if self.consensus_df is None:
         self.logger.error("No consensus map found.")
         return
     data = self.consensus_df.clone()
+    
+    # Filter by mz_range and rt_range if provided
+    if mz_range is not None:
+        data = data.filter((pl.col("mz") >= mz_range[0]) & (pl.col("mz") <= mz_range[1]))
+    if rt_range is not None:
+        data = data.filter((pl.col("rt") >= rt_range[0]) & (pl.col("rt") <= rt_range[1]))
+    
     if colorby not in data.columns:
         self.logger.error(f"Column {colorby} not found in consensus_df.")
         return
@@ -329,7 +340,9 @@ def plot_samples_2d(
     cmap="Turbo256",
     max_features=50000,
     width=900,
-    height=900
+    height=900,
+    mz_range=None,
+    rt_range=None
 ):
     """
     Plot all feature maps for sample_uid in parameter uids in an overlaid scatter plot.
@@ -349,6 +362,8 @@ def plot_samples_2d(
         max_features (int): Maximum number of features to plot (default: 50000)
         width (int): Plot width in pixels (default: 900)
         height (int): Plot height in pixels (default: 900)
+        mz_range (tuple, optional): m/z range for filtering features (min_mz, max_mz)
+        rt_range (tuple, optional): Retention time range for filtering features (min_rt, max_rt)
     """
 
     sample_uids = self._get_sample_uids(samples)
@@ -370,6 +385,12 @@ def plot_samples_2d(
 
     # OPTIMIZATION 1: Batch filter all features for selected samples at once
     features_batch = self.features_df.filter(pl.col("sample_uid").is_in(sample_uids))
+    
+    # Filter by mz_range and rt_range if provided
+    if mz_range is not None:
+        features_batch = features_batch.filter((pl.col("mz") >= mz_range[0]) & (pl.col("mz") <= mz_range[1]))
+    if rt_range is not None:
+        features_batch = features_batch.filter((pl.col("rt") >= rt_range[0]) & (pl.col("rt") <= rt_range[1]))
 
     if features_batch.is_empty():
         self.logger.error("No features found for the selected samples.")

{masster-0.3.2.dist-info → masster-0.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.2
+Version: 0.3.4
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.2.dist-info → masster-0.3.4.dist-info}/RECORD

@@ -19,7 +19,7 @@ masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,
 masster/sample/plot.py,sha256=uUJAd2qxhVG6Ev2hLuU406zFA2TDkkBz2MG12P9fLik,71449
 masster/sample/processing.py,sha256=NjNLt47Fy0UF3Xs35NBhADg57qTC6Lfa4Xz8Y30v83A,58250
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=7ivuAMb3JlFikLOxZjTGwYmuqGehLz9d47gQxfSRtf4,16178
+masster/sample/sample.py,sha256=bsCieIitztHiys7xyyfkKAkyHQRTo9uc0MLq10tsEn0,16178
 masster/sample/sample5_schema.json,sha256=3SPFQZH4SooLYUt_lW-PCOE9rHnl56Vhc2XG-r1nyEQ,3586
 masster/sample/save.py,sha256=o9eFSqqr7KYwvCD3gOJt_nZ4h3pkflWqs0n0oSLM-sU,31970
 masster/sample/sciex.py,sha256=q6PdcjCtV2PWnJiXuvfISu09zjkaTR_fvHvWN9OvOcM,46870
@@ -36,7 +36,7 @@ masster/study/helpers.py,sha256=SeW17rA3BIM2I2Whiye6wegRRSCabIpQoCsjOCafjKw,7488
 masster/study/helpers_optimized.py,sha256=EgOgPaL3c2LA8jDhnlEHvzb7O9Um-vnMIcnNaoH90gA,13620
 masster/study/load.py,sha256=TLxVhXu0HHb51lGggXitQLtfNxz2JJfKMkAXJbxhvhM,46880
 masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
-masster/study/plot.py,sha256=4i3u4geOinCefsambnEGVPF4XuyKTK-_eT5xAWgC7Ik,24045
+masster/study/plot.py,sha256=NW31XdM9Bf5wNvIAs-56AIoPA8VLTqBzr6qJInfZmhc,25159
 masster/study/processing.py,sha256=BQuSBO7O8iTlCjXenECyg0_PAsPF1NNiUllypuemPZI,46101
 masster/study/save.py,sha256=bcRADWTvhTER9WRkT9zNU5mDUPQZkZB2cuJwpRsYmrM,6589
 masster/study/study.py,sha256=5TZgG7tr7mzqHh1tm48V8SEcvRcWiFYG9iDqz0U9ACc,27073
@@ -52,8 +52,8 @@ masster/study/defaults/integrate_chrom_def.py,sha256=Rih3-vat7fHGVfIvRitjNJJI3zL
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
 masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
 masster/study/defaults/study_def.py,sha256=hj8bYtEPwzdowC95yfyoCFt6fZkQePLjpJtmpNz9Z5M,9533
-masster-0.3.2.dist-info/METADATA,sha256=LTK6jfDeryui93xgzncpurTiYrc_iuzRMao82DQ0eMI,44356
-masster-0.3.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.3.2.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.3.2.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.3.2.dist-info/RECORD,,
+masster-0.3.4.dist-info/METADATA,sha256=Uoaha8t5IJHoWFgMcN2w5bci1GT2wtXCbCIoJvCftlg,44356
+masster-0.3.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.3.4.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.3.4.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.3.4.dist-info/RECORD,,