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byemaxx · Sep 20, 2024 · 63608c6 · 63608c6
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diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,52 @@
+
+# Version: 1.114.1
+## Date: 2024-09-19
+### Changes:
+- Change: Optimized the code of Data Preprocessing, split oulier handle and data preprossing to two independent steps.
+
+
+# Version: 1.114.0
+## Date: 2024-09-19
+### Changes:
+- New: Added an option to create taxa table and function table from the OTF only, or from all eligible peptides.
+- Change: 1. Set Outlier handle only apply to peptide level. 2. Change 'None' function to "None_func' in the OTF table to avoid the conflict with the None value. 3.optimize the code of OTF Analyzer.
+- Fix: Fixed some bugs of GUI settings.
+
+# Version: 1.113.4
+## Date: 2024-09-17
+### Changes:
+- Change: move peptide number filter to the class of data preprossing to optimize the code.
+
+# Version: 1.113.3
+## Date: 2024-09-17
+### Changes:
+- Fix: Fixed the data preprossing order of function. Suming peptide to taxa, funcs, taxa-funcs etc. should be before the data preprossing of transform, normalization, or combact.
+
+# Version: 1.113.2
+## Date: 2024-09-17
+### Changes:
+- Change: Changed the default data preprossing after sum peptide to tables, and set only apply outlier handle and combat on peptide level.
+
+# Version: 1.113.1
+## Date: 2024-09-17
+### Changes:
+- Fix: remove epsilon(1e-10) when scale the data with min-max method to avoid the max value is 0.9999999999... rather than 1.0.
+
+# Version: 1.113.0
+## Date: 2024-09-16
+### Changes:
+- New: Added BH method for multiple test correction for t-test, anova, and dnnet's test.
+
+# Version: 1.112.2
+## Date: 2024-09-12
+### Changes:
+- Fix: Fixed the the figsize intialization didn't correctly when multiple monitor was used.
+
+# Version: 1.112.1
+## Date: 2024-09-12
+### Changes:
+- Fix: Fixed the PcoA plot of the beta diversity, the x-axis and y-axis labels were not correct.
+
 # Version: 1.112.0
 ## Date: 2024-09-09
 ### Changes:

diff --git a/Docs/MetaX_Cookbook.assets/Significant_Taxa-Func.png b/Docs/MetaX_Cookbook.assets/Significant_Taxa-Func.png
diff --git a/Docs/MetaX_Cookbook.assets/basic_sankey.png b/Docs/MetaX_Cookbook.assets/basic_sankey.png
diff --git a/Docs/MetaX_Cookbook.assets/set_multi_table.png b/Docs/MetaX_Cookbook.assets/set_multi_table.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.assets/trends_cluster.png b/Docs/MetaX_Cookbook.assets/trends_cluster.png
diff --git a/Docs/MetaX_Cookbook.md b/Docs/MetaX_Cookbook.md
@@ -223,6 +223,34 @@ The Data Overview provides basic information about your data, such as the number
 
 - **Taxa Level:** Select a taxa level for downstream analysis (**Life** in the list means no filtering by any taxa, the follow analysis focus on functions).
 
+- **Split Function:** Split the annotations with multi-functions.
+
+  - | KO                  | Intensity |
+    | ------------------- | --------- |
+    | ko:K00625,ko:K13788 | 10        |
+
+    to
+
+    | KO        | Intensity |
+    | --------- | --------- |
+    | ko:K00625 | 10        |
+    | ko:K13788 | 10        |
+
+    If <u>Share Intensity</u> is checked, the intensity above would given <u>5</u> to each split KO
+
+- **Peptide Number Threshold:**  only keep the taxon (function or OTF) at least has the setting number of peptides.
+
+- **Create Taxa and Func only from OTFs:**
+
+  - **Without selection (checkbox not checked):**
+    - <u>Taxa table:</u> Peptides are filtered based solely on taxa levels, without considering any functional categories.
+    - <u>Function table:</u> Peptides are filtered solely by functional categories and thresholds, regardless of their taxa levels.
+    - <u>Taxa-Function (OTFs) table:</u> Peptides are filtered by both taxa levels and functional categories simultaneously.
+  - **With selection (checkbox checked):**
+
+
+- All tables are filtered by both taxa levels and functional categories simultaneously.
+
 ### Sum Proteins Intensity
 
 Click **Create Proteins Intensity Table** to sum peptides to proteins if the Protein column is in the original table.
@@ -247,9 +275,6 @@ Click **Create Proteins Intensity Table** to sum peptides to proteins if the Pro
 
 ### Data preprocessing
 
-- Data Preprocessing **Before Summing  Peptides**:  Perform data preprocessing first, then sum the peptides to calculate the intensity of each taxon, function and taxa-function pair.
-- Data Preprocessing **After Summing Peptides**: Sum the peptides to calculate the intensity of each taxon, function and taxa-function pair first, then perform data preprocessing for each table.
-
 There are several methods for detecting and handling outliers.
 
 - Two steps will be applied:
@@ -300,7 +325,7 @@ There are several methods for detecting and handling outliers.
   - Here, you can choose a group as the batch effect, then use [<u>reCombat</u>] (https://github.com/BorgwardtLab/reComBat) for handling.
 - **Data Transformation:**
 
-  - Log2, Log10, Square root transformation and Cube root transformation.
+  - Log2, Log10, Square root transformation, Cube root transformation and box-cox.
 
 - **Data Normalization:**
 
@@ -391,7 +416,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
   - Sankey
 
-    - <img src="MetaX_Cookbook.assets/basic_sankey.png" alt="basic_sankey"  />
+    - <img src="MetaX_Cookbook.assets/basic_sankey.png" alt="basic_sankey">
 
 
 
@@ -409,7 +434,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
 - **Add items to Top List:** select the top items to plot by some statistical method.
 
-  - Clicked <u>filter with threshold</u> will filter by the p-value of ANOVA and T-TEST and P-value and Log2FC of DESeq2 result (setting in the corresponding page).
+  - Clicked <u>filter with threshold</u> will filter by the padj of ANOVA and T-TEST and padj and Log2FC of DESeq2 result (setting in the corresponding page).
 
   <img src="./MetaX_Cookbook.assets/add_top_list.png" alt="add_top_list"  />
 
@@ -654,7 +679,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
   - The coloured line is the average 
 
-  <img src="./MetaX_Cookbook.assets/trends_cluster.png" alt="image-20230728144230514"  />
+  <img src="./MetaX_Cookbook.assets/trends_cluster.png" style="zoom: 67%;"  >
 
 
 

diff --git a/Docs/example.ipynb b/Docs/example.ipynb
@@ -91,7 +91,6 @@
     "Parameters:\n",
     "- `level (str)`: The taxonomic level to consider. Default is 's' (species).\n",
     "- `func_threshold (float)`: The threshold for function proportion. Default is 1.00.\n",
-    "- `processing_after_sum (bool)`: Whether to perform data preprocessing after summing protein intensity. Default is False.\n",
     "- `data_preprocess_params (dict)`: Parameters for data preprocessing. Default is {'normalize_method': None, 'transform_method': None,\n",
     "                                    'batch_meta': None, 'outlier_detect_method': None, 'outlier_handle_method': None,\n",
     "                                    'outlier_detect_by_group': None, 'outlier_handle_by_group': None, 'processing_order': None}.\n",

diff --git a/README.md b/README.md
@@ -39,9 +39,7 @@ The desktop version comes fully set up and ready to use, including all required
 ### `Command-line version`:
 Clone the repository to your local machine and install the required dependencies.
   ```bash
-  git clone https://github.com/byemaxx/MetaX.git
-  cd MetaX
-  python -m pip install -r requirements.txt
+  python -m pip install MetaXTools
   ```
 
 

diff --git a/metax/data/example_data/Example_Meta.tsv b/metax/data/example_data/Example_Meta.tsv
@@ -16,17 +16,14 @@ V1_14	V1	ACE005	synthetic	NAS	Acesulfame K
 V1_15	V1	SUC	synthetic	NAS	Sucralose
 V1_16	V1	GLU	dietary sugar	CHO	Glucose (D-Glucose)
 V1_17	V1	NDC	natural extracted	NAS	Neohesperidin Dihydrochalcone
-V1_18	V1	BAS	BAS	BAS	BAS
 V1_19	V1	THA2	synthetic	NAS	Thaumatin
 V1_20	V1	THA03	synthetic	NAS	Thaumatin
 V1_21	V1	REB	natural extracted	NAS	Stevia extract (Rebaudioside A)
 V1_22	V1	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
-V1_23	V1	BAS	BAS	BAS	BAS
 V1_24	V1	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
 V1_25	V1	CYC	synthetic	NAS	Cyclamate (Sodium cyclamate)
 V1_26	V1	PBS	PBS	PBS	PBS
 V1_27	V1	ADV	synthetic	NAS	Advantame
-V1_28	V1	BAS	BAS	BAS	BAS
 V1_29	V1	XYL	sugar alcohols	CHO	Xylitol
 V1_30	V1	STE	natural extracted	NAS	Stevia extract (Stevioside)
 V1_31	V1	LAC	sugar alcohols	CHO	Lactitol (Lactitol monohydrate)
@@ -54,17 +51,14 @@ V2_14	V2	ACE005	synthetic	NAS	Acesulfame K
 V2_15	V2	SUC	synthetic	NAS	Sucralose
 V2_16	V2	GLU	dietary sugar	CHO	Glucose (D-Glucose)
 V2_17	V2	NDC	natural extracted	NAS	Neohesperidin Dihydrochalcone
-V2_18	V2	BAS	BAS	BAS	BAS
 V2_19	V2	THA2	synthetic	NAS	Thaumatin
 V2_20	V2	THA03	synthetic	NAS	Thaumatin
 V2_21	V2	REB	natural extracted	NAS	Stevia extract (Rebaudioside A)
 V2_22	V2	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
-V2_23	V2	BAS	BAS	BAS	BAS
 V2_24	V2	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
 V2_25	V2	CYC	synthetic	NAS	Cyclamate (Sodium cyclamate)
 V2_26	V2	PBS	PBS	PBS	PBS
 V2_27	V2	ADV	synthetic	NAS	Advantame
-V2_28	V2	BAS	BAS	BAS	BAS
 V2_29	V2	XYL	sugar alcohols	CHO	Xylitol
 V2_30	V2	STE	natural extracted	NAS	Stevia extract (Stevioside)
 V2_31	V2	LAC	sugar alcohols	CHO	Lactitol (Lactitol monohydrate)
@@ -92,17 +86,14 @@ V3_14	V3	ACE005	synthetic	NAS	Acesulfame K
 V3_15	V3	SUC	synthetic	NAS	Sucralose
 V3_16	V3	GLU	dietary sugar	CHO	Glucose (D-Glucose)
 V3_17	V3	NDC	natural extracted	NAS	Neohesperidin Dihydrochalcone
-V3_18	V3	BAS	BAS	BAS	BAS
 V3_19	V3	THA2	synthetic	NAS	Thaumatin
 V3_20	V3	THA03	synthetic	NAS	Thaumatin
 V3_21	V3	REB	natural extracted	NAS	Stevia extract (Rebaudioside A)
 V3_22	V3	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
-V3_23	V3	BAS	BAS	BAS	BAS
 V3_24	V3	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
 V3_25	V3	CYC	synthetic	NAS	Cyclamate (Sodium cyclamate)
 V3_26	V3	PBS	PBS	PBS	PBS
 V3_27	V3	ADV	synthetic	NAS	Advantame
-V3_28	V3	BAS	BAS	BAS	BAS
 V3_29	V3	XYL	sugar alcohols	CHO	Xylitol
 V3_30	V3	STE	natural extracted	NAS	Stevia extract (Stevioside)
 V3_31	V3	LAC	sugar alcohols	CHO	Lactitol (Lactitol monohydrate)
@@ -130,17 +121,14 @@ V4_14	V4	ACE005	synthetic	NAS	Acesulfame K
 V4_15	V4	SUC	synthetic	NAS	Sucralose
 V4_16	V4	GLU	dietary sugar	CHO	Glucose (D-Glucose)
 V4_17	V4	NDC	natural extracted	NAS	Neohesperidin Dihydrochalcone
-V4_18	V4	BAS	BAS	BAS	BAS
 V4_19	V4	THA2	synthetic	NAS	Thaumatin
 V4_20	V4	THA03	synthetic	NAS	Thaumatin
 V4_21	V4	REB	natural extracted	NAS	Stevia extract (Rebaudioside A)
 V4_22	V4	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
-V4_23	V4	BAS	BAS	BAS	BAS
 V4_24	V4	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
 V4_25	V4	CYC	synthetic	NAS	Cyclamate (Sodium cyclamate)
 V4_26	V4	PBS	PBS	PBS	PBS
 V4_27	V4	ADV	synthetic	NAS	Advantame
-V4_28	V4	BAS	BAS	BAS	BAS
 V4_29	V4	XYL	sugar alcohols	CHO	Xylitol
 V4_30	V4	STE	natural extracted	NAS	Stevia extract (Stevioside)
 V4_31	V4	LAC	sugar alcohols	CHO	Lactitol (Lactitol monohydrate)
@@ -168,17 +156,14 @@ V5_14	V5	ACE005	synthetic	NAS	Acesulfame K
 V5_15	V5	SUC	synthetic	NAS	Sucralose
 V5_16	V5	GLU	dietary sugar	CHO	Glucose (D-Glucose)
 V5_17	V5	NDC	natural extracted	NAS	Neohesperidin Dihydrochalcone
-V5_18	V5	BAS	BAS	BAS	BAS
 V5_19	V5	THA2	synthetic	NAS	Thaumatin
 V5_20	V5	THA03	synthetic	NAS	Thaumatin
 V5_21	V5	REB	natural extracted	NAS	Stevia extract (Rebaudioside A)
 V5_22	V5	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
-V5_23	V5	BAS	BAS	BAS	BAS
 V5_24	V5	MAN	sugar alcohols	CHO	Mannitol (D-Mannitol)
 V5_25	V5	CYC	synthetic	NAS	Cyclamate (Sodium cyclamate)
 V5_26	V5	PBS	PBS	PBS	PBS
 V5_27	V5	ADV	synthetic	NAS	Advantame
-V5_28	V5	BAS	BAS	BAS	BAS
 V5_29	V5	XYL	sugar alcohols	CHO	Xylitol
 V5_30	V5	STE	natural extracted	NAS	Stevia extract (Stevioside)
 V5_31	V5	LAC	sugar alcohols	CHO	Lactitol (Lactitol monohydrate)