diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml
index a97fb0b..17e7b21 100644
--- a/.github/workflows/jekyll-gh-pages.yml
+++ b/.github/workflows/jekyll-gh-pages.yml
@@ -68,7 +68,7 @@ jobs:
html_content = markdown.markdown(markdown_content, extensions=['tables', 'toc'])
# Add Bootstrap classes to tables and images
- html_content = re.sub(r'', r'
', html_content)
+ html_content = re.sub(r'', r'', html_content)
html_content = re.sub(r'', r'', html_content)
# Jinja2 template for HTML output
diff --git a/Docs/MetaX_Cookbook.md b/Docs/MetaX_Cookbook.md
index 1d3af23..f699670 100644
--- a/Docs/MetaX_Cookbook.md
+++ b/Docs/MetaX_Cookbook.md
@@ -27,11 +27,11 @@ Visit **Github** to get more information:
- The main window of MetaX
-
+
- Click 'Tools Menu' to switch different tool
-
+
# Module 1. Database Builder
@@ -43,13 +43,13 @@ Visit **Github** to get more information:
-
+
**(Option 2) Build Database By Own Data**
+ (1). **Annotation Table:** a TSV table(separated by a tab), and make sure the first column is protein name joined Genome by "_", e.g. "Genome1_protein1" and other columns are annotation information.
-
+
- (2). **Taxa Table:** a TSV table(separated by a tab), and make sure the first column is Genome name,e.g. "Genome1" and the second column is taxa.
- **Example Annotation Table:**
@@ -87,7 +87,7 @@ Visit **Github** to get more information:
- Update the built database, and extend more annotations.
-
+
+ **(Option 1) By built-in mode:**
@@ -117,7 +117,7 @@ Visit **Github** to get more information:
- Annotate the peptide to TaxaFunc before analyzing by **Peptide Annotator**
-
+
You have to provide:
@@ -173,7 +173,7 @@ When we get the **Operational Taxa-Functions (OTF) Table** after using the **
There, we can simply load the example data by **clicking the button**.
-
+
Then, click **Go** to start the analysis.
@@ -183,17 +183,17 @@ Data Overview includes some basic information about your data, such as the numbe
We can set the threshold of linked peptides and the differences between them to plot the figure.
-
+
We Can Select different functions to plot the proportion distribution.
-
+
We can also filter some samples for downstream analysis.
-
+
@@ -201,7 +201,7 @@ We can also filter some samples for downstream analysis.
## 3. Set TaxaFunc
-
+
### Data selection
@@ -234,14 +234,15 @@ We can click **Create Proteins Intensity Table** to sum the peptide to the prote
There are several methods for detecting and handling outliers.
- Two steps will be applied:
- 1. Outlier Detection: Users can select a method to mark outlier values as NaN. Then the rows `only contain NaN values and 0` will be removed. The remaining NaN values will be handled in the next step.
- 2. Outlier Handling: Users can choose a method to fill the remaining NaN values.
+ - Outlier Detection: Users can select a method to mark outlier values as NaN. Then the rows `only contain NaN values and 0` will be removed. The remaining NaN values will be handled in the next step.
+ - Outlier Handling: Users can choose a method to fill the remaining NaN values.
+
- **Outliers Detection:**
-- - **IQR:** In a group, if the value is greater than Q3+1.5\*IQR or less than Q1-1.5\*IQR, the value will be marked as NaN.
+ - **IQR:** In a group, if the value is greater than Q3+1.5\*IQR or less than Q1-1.5\*IQR, the value will be marked as NaN.
- **Missing-Value:** Detect nan values in the data. If a value is nan, it will be marked as a NaN.
@@ -298,9 +299,9 @@ There are several methods for detecting and handling outliers.
Then we can check tables in **Table Review** part, and export it.
-
+
-
+
@@ -308,15 +309,15 @@ Then we can check tables in **Table Review** part, and export it.
### PCA, Correlation and Box Plot
-
+
We can select **meta** **groups** or **samples** (default all) to plot **PCA**, **Correlation**, and **Box Plot** for **[Taxa, Function, Taxa-Func, Peptide table, Protein table**]
-
+
-
+
-
+
@@ -334,47 +335,47 @@ We can select **meta** **groups** or **samples** (default a
**e.g. :** Select PBS, BAS and others groups **only in** Individual V1
- -
+ -
- Select **specific Samples** to Analysis
- -
+ -
- ![image-20230728112519665](./MetaX_Cookbook.assets/right_cilck_menu.png)
- -
+ -
- **Number stats**
- We can plot the bar for the number for each table by **groups** or by **samples**
-
+
- **Taxa Specific**
- Alpha/Beta Diversity
- -
- -
+ -
+ -
- Sunburst
- -
+ -
- TreeMap
- -
+ -
- Sankey
- -
+ -
### Heatmap and Bar Plot
-
+
- **Select items(Taxa, Function, Taxa-Func and Peptide ) to plot:**
- Add **All Taxa**, or select one we are interested in.
@@ -393,7 +394,7 @@ We can select **meta** **groups** or **samples** (default a
- Make sure one row one item
-
+
@@ -412,21 +413,21 @@ We can select **meta** **groups** or **samples** (default a
- **For Bar**
- **Bar Ldg**: Show the legend when plotting Bar
- **Bar %:** Transfer each col to percent when plotting Bar
- -
+ -
- Plot all color maps to view by right click **Theme**
- ![right_click_theme](MetaX_Cookbook.assets/right_click_theme.png)
- -
+ -
- **Plot:**
-
+
- **Modify** the pic to fit the window to get the **Perfect picture**:
-
+
- -
+ -
@@ -434,22 +435,22 @@ We can select **meta** **groups** or **samples** (default a
- **Bar Plot:**
-
+
- **interactive function:**
-
+
- change to line plot:
-
+
- 3D Bar plot
- Plot 3D bar by selecting a **sub meta**.
- ![basic_stats_bar_3d_setting](MetaX_Cookbook.assets/basic_stats_bar_3d_setting.png)
- -
+ -
@@ -457,7 +458,7 @@ We can select **meta** **groups** or **samples** (default a
- Query everything of a peptide
-
+
@@ -471,13 +472,13 @@ We can select **meta** **groups** or **samples** (default a
- Select 2 group stats T-Test for **[Taxa, Function, Taxa-Func, Peptide table and Proteins Table**]
-
+
### ANOVA-TEST
- select some groups or all groups to ANOVA Test for **[Taxa, Function, Taxa-Func and Peptide table**]
-
+
### Significant Taxa-Func
@@ -488,7 +489,7 @@ We can select **meta** **groups** or **samples** (default a
- The **result** of the T-test and ANOVA Test will show in a new window
-
+
@@ -496,18 +497,18 @@ We can select **meta** **groups** or **samples** (default a
- Chose a Table to plot **top differences heatmap** or get **the top table**
-
+
- Taxa-Func cross heatmap:
- The orange cells mean in the corresponding function ( X-axis) and Taxa( Y-axis) are significantly different between groups.
-
+
- Func(Taxa) Heatmap:
- The colour shows the intensity of the significant Func(Taxa) between groups.
-
+
- Significant Taxa-Func Heatmap:
@@ -520,7 +521,7 @@ We can select **meta** **groups** or **samples** (default a
### TUKEY_TEST
-
+
- **Select a function:**
@@ -534,7 +535,7 @@ We can select **meta** **groups** or **samples** (default a
- Test the significant groups in this function and this taxon.
-
+
- Show Linked Taxa Only: only shows the taxa linked with the current function in the taxa combo box.
@@ -547,7 +548,7 @@ We can select **meta** **groups** or **samples** (default a
- **Tukey result plot:**
- The dots and lines show the difference in the mean value of the Tukey test
-
+
### Group-Control TEST
@@ -560,7 +561,7 @@ We can select **meta** **groups** or **samples** (default a
- ![group_control_test](./MetaX_Cookbook.assets/group_control_test.png)
- Result of Dunnett's Test:
- T- Statistic value shown in the heatmap
- -
+ -
@@ -572,7 +573,7 @@ We can select **meta** **groups** or **samples** (default a
-
+
- Select p-adjust, log2FC to plot
@@ -580,19 +581,19 @@ We can select **meta** **groups** or **samples** (default a
- Volcano:
-
+
- Sankey:
- The last node level is the functions linked to each Taxon (When plotting Taxa-Func)
-
+
### Co-Expression Networks
- select Groups or Samples to calculate the correlation and plot the network
-
+
- Slecet table, and set the method of correlation and threshold
@@ -600,7 +601,7 @@ We can select **meta** **groups** or **samples** (default a
- Add some items to the focus list (Optional)
-
+
- Network Plot
@@ -608,7 +609,7 @@ We can select **meta** **groups** or **samples** (default a
- The depth of green represents the correlation value
- The size of the dot indicates the number of connections
-
+
@@ -616,13 +617,13 @@ We can select **meta** **groups** or **samples** (default a
- Add items to the list window to plot the clusters with similar trends of intensity
-
+
- Clusters plot (clustered by **k-means**)
- The coloured line is the average
-
+
@@ -632,7 +633,7 @@ We can select **meta** **groups** or **samples** (default a
- The dashed red line is the average
-
+
@@ -644,7 +645,7 @@ We can select **meta** **groups** or **samples** (default a
### Taxa-Func Link Plot
-
+
- Check all taxa in one function (or Check all functions in a taxon)
@@ -652,7 +653,7 @@ We can select **meta** **groups** or **samples** (default a
- **Linked Number**: The number shows how many taxa are linked in this function
- **The number starts with Taxa**: The number shows how many peptides are in this Taxa-Func
-
+
- Filter items of the Taxa and Func list
@@ -664,30 +665,30 @@ We can select **meta** **groups** or **samples** (default a
- Select some groups (Default all) to get **the intensity of each taxon of this function**
-
+
-
+
- Plot **peptides** in one Function of a Taxon
-
+
-
+
- Switch Bar to Stacked or not ( Line)
-
+
- Change Bar plot to Lines
-
+
### Taxa-Func Network
- Select some groups or samples (default all)
- add some taxa, func or taxa-func to focus the window (Optional)
-
+
- Plot list only
- Checked the "**Plot List Only**" to show the items only in the list
@@ -697,7 +698,7 @@ We can select **meta** **groups** or **samples** (default a
- The red dots are the taxa we focused on
- The green dots are the functions we focused on
-
+
@@ -719,7 +720,7 @@ We can select **meta** **groups** or **samples** (default a
- **Show or Hide the Console**
- -
+ -
- **Any Table Mode**