Merge branch 'dev'

byemaxx · Jul 15, 2024 · c22341d · c22341d
2 parents 6191599 + 67add1f
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diff --git a/.gitignore b/.gitignore
@@ -2,9 +2,12 @@
 .vscode/
 .idea/
 .trunk/
-tests/
+local_tests/
 *.pyc
 *.db
 .gitignore
 .gitattributes
-todo.md
+dist
+MetaXTools.egg-info
+.pypirc
+README_PyPi.md
diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,37 @@
+# Version: 1.108.7
+## Date: 2024-07-14
+### Changes:
+- Change: Optimized Peptide Annotator, changed them to class method for better performance.
+
+
+# Version: 1.108.6
+## Date: 2024-07-11
+### Changes:
+- Change: Optimized file structure and code structure, make easlier to install and run the MetaX by pip or conda.
+
+
+# Version: 1.108.5
+## Date: 2024-07-11
+### Changes:
+- Fix: Fixed the Settting window was not able to minimize (Not perfect yet, need to be fixed in the future).
+
+# Version: 1.108.2
+## Date: 2024-07-08
+### Changes:
+- Fix: Fixed the bug of when int number in the meta table, the protential error will raise.
+
+
+# Version: 1.108.1
+## Date: 2024-06-27
+### Changes:
+- New: Add Sub Meta option for the basic Heatmap plot.
+
+
+# Version: 1.108.0
+## Date: 2024-06-27
+### Changes:
+- New: Enable multiple selection for the in condition group box.
+
 # Version: 1.107.8
 ## Date: 2024-06-26
 ### Changes:

diff --git a/Docs/MetaX_Cookbook.assets/basic_stats_heatmap.png b/Docs/MetaX_Cookbook.assets/basic_stats_heatmap.png
diff --git a/Docs/MetaX_Cookbook.assets/basic_stats_heatmap_seeting.png b/Docs/MetaX_Cookbook.assets/basic_stats_heatmap_seeting.png
diff --git a/Docs/MetaX_Cookbook.assets/main_window.png b/Docs/MetaX_Cookbook.assets/main_window.png
diff --git a/Docs/MetaX_Cookbook.assets/settings.png b/Docs/MetaX_Cookbook.assets/settings.png
diff --git a/Docs/MetaX_Cookbook.assets/settings_page2.png b/Docs/MetaX_Cookbook.assets/settings_page2.png
diff --git a/Docs/MetaX_Cookbook.md b/Docs/MetaX_Cookbook.md
@@ -23,7 +23,7 @@ Visit **Github** to get more information:
 
 
 
-# Get Start
+# Getting Started
 
 - The main window of MetaX
 
@@ -230,19 +230,20 @@ Click **Create Proteins Intensity Table** to sum peptides to proteins if the Pro
 - **Occam's Razor**, **Anti-Razor** and **Rank:** Methods available for inferring shared peptides.
   - Razor:
     1. Build a minimal set of proteins to cover all peptides.
-    2. For each peptide, choose the protein which has most peptides (if multiple proteins have the same number of peptides, share intensity to them).
+    2. For each peptide, choose the protein with the most peptides (if multiple proteins have the same number of peptides, share intensity to them).
   - Anti-Razor:
-    - All proteins are shared the intensity of each peptide.
+    - All proteins share the intensity of each peptide.
   - Rank:
     1. Build the rank of proteins.
     2. Choose the protein with a higher rank for the shared peptide.
-
-
-- **Methods to Build Protein Rank:**
-  - unique_counts: Use the counts of proteins inferred by unique peptides.
-  - all_count: Use the counts of all proteins.
-  - unique_intensity: Use the intensity of proteins inferred by unique peptides.
-  - shared_intensity: Use the intensity divided by the number of shared peptides for each protein.
+
+
+    - **Methods to Build Protein Rank:**
+      - unique_counts: Use the counts of proteins inferred by unique peptides.
+      - all_count: Use the counts of all proteins.
+      - unique_intensity: Use the intensity of proteins inferred by unique peptides.
+      - shared_intensity: Use the intensity divided by the number of shared peptides for each protein.
+
 
 ### Data preprocessing
 
@@ -424,6 +425,8 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
   - **Rename Samples**: Add group info to each sample name
   - **Rename Taxa**: Only keep the last taxonomic level to reduce to name
   - **Plot Mean**: calculate the mean of each group before plotting
+
+  - **Sub Meta:** select a second meta, then combine two meta by mean for Heatmap and 3D bar plot
     - **<u>For Heatmap</u>**
       - **Theme**: The theme of the heatmap
       - **scale**: Scale method of the heatmap