msreport 0.0.24__py3-none-any.whl → 0.0.26__py3-none-any.whl

msreport/__init__.py

@@ -10,4 +10,4 @@ import msreport.normalize
 import msreport.plot
 import msreport.reader
 
-__version__ = "0.0.24"
+__version__ = "0.0.26"

msreport/helper/table.py

@@ -176,12 +176,22 @@ def find_sample_columns(
             columns.
 
     Returns:
-        A list of sample column names.
+        A list of column names containing the substring and any entry of 'samples'.
+        Columns are returned in the order of entries in 'samples'.
     """
+    WHITESPACE_CHARS = " ."
+
     matched_columns = []
-    for column in find_columns(table, substring):
-        if any([sample in column for sample in samples]):
-            matched_columns.append(column)
+    substring_columns = find_columns(table, substring)
+    for sample in samples:
+        sample_columns = [c for c in substring_columns if sample in c]
+        for col in sample_columns:
+            column_remainder = (
+                col.replace(substring, "").replace(sample, "").strip(WHITESPACE_CHARS)
+            )
+            if column_remainder == "":
+                matched_columns.append(col)
+                break
     return matched_columns
 
 

msreport/plot.py

@@ -718,7 +718,10 @@ def volcano_ma(
         )
 
         ax.set_xlabel(x_variable)
-        ax.set_ylabel(f"{y_variable} [-log10]")
+        if y_variable == pvalue_tag:
+            ax.set_ylabel(f"{y_variable} [-log10]")
+        else:
+            ax.set_ylabel(f"{y_variable} [log2]")
 
     fig.tight_layout()
     return fig, axes
@@ -1075,13 +1078,13 @@ def pvalue_histogram(
         )
 
         # Adjust x- and y-axis
-        ax.set_xlabel(None)
         ax.set_xticks(np.arange(0, 1.01, 0.5))
         ax.tick_params(labelsize=9)
         if plot_number > 0:
             ax.tick_params(axis="y", color="none")
 
-        # Add second label
+        # Add x-label and second y-label
+        ax.set_xlabel(pvalue_tag, fontsize=9)
         ax2 = ax.twinx()
         ax2.set_yticks([])
         ax2.set_ylabel(comparison_group, fontsize=9)

msreport/qtable.py

@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import Any, Optional
+from typing import Any, Iterable, Optional
 import os
 import warnings
 
@@ -196,8 +196,9 @@ class Qtable:
         columns = helper.find_sample_columns(self.data, tag, samples)
         table = self.get_data(exclude_invalid=exclude_invalid)[columns]
         if samples_as_columns:
-            mapping = _str_to_substr_mapping(columns, samples)
-            table.rename(columns=mapping, inplace=True)
+            sample_to_columns = _match_samples_to_tag_columns(samples, columns, tag)
+            columns_to_samples = {v: k for k, v in sample_to_columns.items()}
+            table.rename(columns=columns_to_samples, inplace=True)
         return table
 
     def make_expression_table(
@@ -502,15 +503,30 @@ def _exclude_invalid(df: pd.DataFrame) -> pd.DataFrame:
     return df[df["Valid"]].copy()
 
 
-def _str_to_substr_mapping(strings, substrings) -> dict[str, str]:
-    """Mapping of strings to substrings.
+def _match_samples_to_tag_columns(
+    samples: Iterable[str],
+    columns: Iterable[str],
+    tag: str,
+) -> dict:
+    """Mapping of samples to columns which contain the sample and the tag.
 
-    Strings point to a matching substring. If multiple substrings are found in a string,
-    only one is reported.
+    Args:
+        samples: A list of sample names.
+        columns: A list of column names.
+        tag: A string that must be present in the column names.
+
+    Returns:
+        A dictionary that maps sample names to column names that contain the sample
+        name and the tag.
     """
+    WHITESPACE_CHARS = " ."
+
     mapping = dict()
-    for sub in substrings:
-        mapping.update({s: sub for s in strings if sub in s})
+    for sample in samples:
+        for col in columns:
+            if col.replace(tag, "").replace(sample, "").strip(WHITESPACE_CHARS) == "":
+                mapping[sample] = col
+                break
     return mapping
 
 

msreport/reader.py

@@ -2196,9 +2196,11 @@ def extract_fragpipe_localization_probabilities(localization_entry: str) -> dict
         _, probabilities = msreport.peptidoform.parse_modified_sequence(
             probability_sequence, "(", ")"
         )
-        modification_probabilities[modification] = {
-            site: float(probability) for site, probability in probabilities
-        }
+        if modification not in modification_probabilities:
+            modification_probabilities[modification] = {}
+        modification_probabilities[modification].update(
+            {site: float(probability) for site, probability in probabilities}
+        )
     return modification_probabilities
 
 

{msreport-0.0.24.dist-info → msreport-0.0.26.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: msreport
-Version: 0.0.24
+Version: 0.0.26
 Summary: Post processing and analysis of quantitative proteomics data
 Author-email: "David M. Hollenstein" <hollenstein.david@gmail.com>
 License: Apache-2.0

{msreport-0.0.24.dist-info → msreport-0.0.26.dist-info}/RECORD

@@ -1,4 +1,4 @@
-msreport/__init__.py,sha256=9Zyj1HfxCZFhrNmvHluUpPe70tZZJwQxSbALKzKqGj8,343
+msreport/__init__.py,sha256=plg-xX45MtHFaMW2qKkNZMTku2gH1Eu5iY4mmFdYSa8,343
 msreport/analyze.py,sha256=JBLuFLYJjI-8NIIwzq2gEJKJYFmKyuLUwf8NgSzC9_c,25350
 msreport/errors.py,sha256=qJan3lzRX6uwnByg9LfAfGKEKC2tm9SYUBvk3TdH_AM,300
 msreport/export.py,sha256=pyB8D1VjvfJWO6ka6uMnHsbc6SRlmCyhUB2sfBlhYDQ,20095
@@ -7,9 +7,9 @@ msreport/impute.py,sha256=UJXfni8xjfIrdaq-tIa9MOyklHLQxq-LHRlbHi7G5IM,10441
 msreport/isobar.py,sha256=H6AJA81AJQ-gGoc8NEFpNAe6ofwzoK4BGnxQHZ80GlA,6551
 msreport/normalize.py,sha256=fQx1QQxusrfddcA_oATz88_ojOqClLQVxNNoJxdOOX4,19334
 msreport/peptidoform.py,sha256=C0IWyvnKivGyizkrtpA_i_lLgw8YZgIxuFBtURrE6rw,11879
-msreport/plot.py,sha256=q21AdLatXGLPSgD0jKYebnygMhm_c7I9Efv8Xa7sqo0,43865
-msreport/qtable.py,sha256=o5_yAmSvs1yv8DgJH7LGDaR4ArLLgcLwdII2zlfkOFg,22420
-msreport/reader.py,sha256=m550jNjJxzaORbR_fI6wB87WSY6bAjxtWuo8BSebigM,104847
+msreport/plot.py,sha256=MUWYSzNKRct9JYDQE7uL_zLxlG8vjTS2so9e4EXyvHw,44005
+msreport/qtable.py,sha256=g9hrVyUdQbiNkBnnFNp4JXNiEAEb_yddrefy34gYMgM,22947
+msreport/reader.py,sha256=PngSiFqX0uFcXCwyU9lwKANGgG8PeoejpcMB3EmlvQc,104972
 msreport/aggregate/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 msreport/aggregate/condense.py,sha256=sNBEsSqCej-zvzd8QeyaScBxUnP_UcaZWzQx9dvRAD8,5860
 msreport/aggregate/pivot.py,sha256=tCxdhSdXAgEobnsp-n2DX91PwTiNYbx_FYgY6SOef4M,5079
@@ -17,14 +17,14 @@ msreport/aggregate/summarize.py,sha256=aI0YP9Kg4ZTVjS6c9gzu3xqvLOTsYJ5ZT3FcUJyg1
 msreport/helper/__init__.py,sha256=8B7gdXn5tFeZATBF30TMaWu0ppc7xFa72JLxMYt_qUM,535
 msreport/helper/calc.py,sha256=ReMP1jA7bz-a7J1DdlAVATN9zjSXENqbw652WfjSEkY,4088
 msreport/helper/maxlfq.py,sha256=DE9yX4vjMRSmolffrpC9UkCXmSs-rCN15cnlNzma4zw,14938
-msreport/helper/table.py,sha256=xAp1me8c6bllfLk27JCl2mFq6fL7jAe4Ic8Gw2yNhf4,11037
+msreport/helper/table.py,sha256=N-veDU3vQ2NeOfKcxUop5SfCv2iW038akkSKxU2yjzg,11464
 msreport/helper/temp.py,sha256=jNulgDATf9sKXEFWMXAhjflciOZPAqlxg_7QZS7IkW8,3736
 msreport/rinterface/__init__.py,sha256=Z1I-4buERXTPIZmhdaTKZWfbJv_qVcqnUVqIJZx1Du8,146
 msreport/rinterface/limma.py,sha256=ATtsVyGSnqUGkyodQTgdpIFhEb4dJZ6wvSjrRsCrNRY,5421
 msreport/rinterface/rinstaller.py,sha256=sm6CJD0-XSxdDpUnL9EAI_CAIgo1NucYxPI9gL93zqw,1377
 msreport/rinterface/rscripts/limma.R,sha256=gr_yjMm_YoG45irDhWOo6gkRQSTwj_7uU_p3NBRHPm8,4331
-msreport-0.0.24.dist-info/licenses/LICENSE.txt,sha256=Pd-b5cKP4n2tFDpdx27qJSIq0d1ok0oEcGTlbtL6QMU,11560
-msreport-0.0.24.dist-info/METADATA,sha256=JBfnxTvf3tal-1UgCJvocxpN79vvSP6c0O7_HOMt_lE,5339
-msreport-0.0.24.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
-msreport-0.0.24.dist-info/top_level.txt,sha256=Drl8mCckJHFIw-Ovh5AnyjKnqvLJltDOBUr1JAcHAlI,9
-msreport-0.0.24.dist-info/RECORD,,
+msreport-0.0.26.dist-info/licenses/LICENSE.txt,sha256=Pd-b5cKP4n2tFDpdx27qJSIq0d1ok0oEcGTlbtL6QMU,11560
+msreport-0.0.26.dist-info/METADATA,sha256=0OpBlUdIaAqhdzEK9Mkq12rVJpeJHuYflFI4griTxqE,5339
+msreport-0.0.26.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
+msreport-0.0.26.dist-info/top_level.txt,sha256=Drl8mCckJHFIw-Ovh5AnyjKnqvLJltDOBUr1JAcHAlI,9
+msreport-0.0.26.dist-info/RECORD,,