Merge pull request #103 from MannLabs/multicova

Multicova

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.0
+current_version = 0.4.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

HISTORY.md

@@ -1,5 +1,10 @@
 # Changelog
 
+# 0.4.0
+* SAM implementation from Isabel (MultiCova) 
+* Volcano Plot with permutation based FDR line
+* Bug fix when reseting matrix and saving info
+
 # 0.3.0
 * One Click Installer for macOS, Linux and Windows
 * Spectronaut support

alphastats/DataSet.py

@@ -109,7 +109,8 @@ def _remove_misc_samples_in_metadata(self):
             )
 
     def create_matrix(self):
-        """Creates a matrix of the Outputfile, with columns displaying features (Proteins) and
+        """
+        Creates a matrix of the Outputfile, with columns displaying features (Proteins) and
         rows the samples.
         """
 
@@ -126,7 +127,7 @@ def create_matrix(self):
         # remove proteins with only zero
         self.mat = mat.loc[:, (mat != 0).any(axis=0)]
         # reset preproccessing info
-        self._save_dataset_info()
+        self.preprocessing_info = self._save_dataset_info()
         self.preprocessed = False
         self.rawmat = mat
 

alphastats/DataSet_Plot.py

@@ -104,18 +104,22 @@ def plot_volcano(
         min_fc=1,
         alpha=0.05,
         draw_line=True,
+        perm=100, 
+        fdr=0.05
     ):
         """Plot Volcano Plot
 
         Args:
             column (str): column name in the metadata file with the two groups to compare
             group1 (str/list): name of group to compare needs to be present in column or list of sample names to compare
             group2 (str/list): name of group to compare needs to be present in column  or list of sample names to compare
-            method (str): "anova", "wald", "ttest", Defaul ttest.
+            method (str): "anova", "wald", "ttest", "SAM" Defaul ttest.
             labels (bool): Add text labels to significant Proteins, Default False.
             alpha(float,optional): p-value cut off.
             min_fc (float): Minimum fold change
             draw_line(boolean): whether to draw cut off lines.
+            perm(float,optional): number of permutations when using SAM as method. Defaults to 100.
+            fdr(float,optional): FDR cut off when using SAM as method. Defaults to 0.05.
 
 
         Returns:
@@ -132,6 +136,8 @@ def plot_volcano(
             min_fc=min_fc,
             alpha=alpha,
             draw_line=draw_line,
+            perm=perm, 
+            fdr=fdr
         )
 
         return volcano_plot.plot

alphastats/DataSet_Statistics.py

@@ -105,9 +105,11 @@ def diff_expression_analysis(self, group1, group2, column=None, method="ttest"):
         elif method == "ttest":
             test = de.test.t_test(data=d, grouping=column)
 
+        #elif method == "SAM":
+
         else:
             raise ValueError(
-                f"{method} is invalid choose between 'wald' for Wald-test and 'ttest'"
+                f"{method} is invalid choose between 'wald' for Wald-test, 'SAM' and 'ttest'"
             )
 
         df = test.summary().rename(columns={"gene": self.index_column})

alphastats/__init__.py

@@ -1,5 +1,5 @@
 __project__ = "alphastats"
-__version__ = "0.3.0"
+__version__ = "0.4.0"
 __license__ = "Apache"
 __description__ = "An open-source Python package for Mass Spectrometry Analysis"
 __author__ = "Mann Labs"

alphastats/gui/pages/04_Analysis.py

@@ -1,8 +1,7 @@
 import streamlit as st
 from alphastats.gui.utils.analysis_helper import (
     get_analysis,
-    load_options,
-)  # , check_if_options_are_loaded
+)  
 from alphastats.gui.utils.ui_helper import sidebar_info
 import alphastats.gui.utils.analysis_helper
 import pandas as pd
@@ -139,17 +138,15 @@ def select_analysis():
         if method in st.session_state.plotting_options.keys():
 
             analysis_result = get_analysis(
-
                 method=method, options_dict=st.session_state.plotting_options
             )
-
             plot_to_display = True
 
         elif method in st.session_state.statistic_options.keys():
 
             analysis_result = get_analysis(
-            method=method, options_dict=st.session_state.statistic_options
-        )
+                method=method, options_dict=st.session_state.statistic_options
+            )
             df_to_display = True
 
         st.markdown("")

alphastats/gui/utils/analysis_helper.py

@@ -1,4 +1,3 @@
-from tkinter import E
 import pandas as pd
 import logging
 import streamlit as st
@@ -93,7 +92,7 @@ def gui_volcano_plot():
     chosen_parameter_dict = helper_compare_two_groups()
     method = st.selectbox(
         "Differential Analysis using:",
-        options=["ttest", "anova", "wald"],
+        options=["ttest", "anova", "wald", "sam"],
     )
     chosen_parameter_dict.update({"method": method})
 
@@ -116,6 +115,16 @@ def gui_volcano_plot():
             "min_fc": min_fc,
         }
 
+    if method == "sam":
+        perm = st.number_input(
+            label="Number of Permutations", min_value=1, max_value=1000, value=10
+        )
+        fdr = st.number_input(
+            label="FDR cut off", min_value=0.005, max_value=0.1, value=0.050
+        )
+        chosen_parameter_dict.update({"perm": perm, "fdr": fdr})
+
+
     submitted = st.button("Submit")
 
     if submitted: