From b2e7a986976234f0abb2e8d45cbdded1235ea6f7 Mon Sep 17 00:00:00 2001 From: Qing <44231502+byemaxx@users.noreply.github.com> Date: Mon, 3 Jun 2024 16:04:48 -0400 Subject: [PATCH] updated styles of the cookbook --- .github/workflows/jekyll-gh-pages.yml | 2 +- Docs/MetaX_Cookbook.md | 143 +++++++++++++------------- 2 files changed, 73 insertions(+), 72 deletions(-) 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 - main_window + main_window - Click 'Tools Menu' to switch different tool - tools_menu + tools_menu # Module 1. Database Builder @@ -43,13 +43,13 @@ Visit **Github** to get more information: -dbbuilder +dbbuilder **(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. -dbbuilder_own +dbbuilder_own - (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. -db_updater +db_updater + **(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** - peptide2taxafunc + peptide2taxafunc 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**. -load_example +load_example 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. -data_overview +data_overview We Can Select different functions to plot the proportion distribution. -data_overview_func +data_overview_func We can also filter some samples for downstream analysis. -data_overview_filter +data_overview_filter @@ -201,7 +201,7 @@ We can also filter some samples for downstream analysis. ## 3. Set TaxaFunc -set_multi_table +set_multi_table ### 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. -table_review +table_review -table_review_open_window +table_review_open_window @@ -308,15 +309,15 @@ Then we can check tables in **Table Review** part, and export it. ### PCA, Correlation and Box Plot -basic_stats_pca +basic_stats_pca 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**] -pca +pca -pca_3d +pca_3d -correlation +correlation boxplot @@ -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 - - group_in_condition + - group_in_condition - Select **specific Samples** to Analysis - - image-20230728113359732 + - image-20230728113359732 - ![image-20230728112519665](./MetaX_Cookbook.assets/right_cilck_menu.png) - - image-20230728112747731 + - image-20230728112747731 - **Number stats** - We can plot the bar for the number for each table by **groups** or by **samples** - basic_number + basic_number - **Taxa Specific** - Alpha/Beta Diversity - - alpha_div - - beta_div + - alpha_div + - beta_div - Sunburst - - sunburst + - sunburst - TreeMap - - treemap + - treemap - Sankey - - basic_sankey + - basic_sankey ### Heatmap and Bar Plot -basic_stats_heatmap +basic_stats_heatmap - **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 -add_a_list +add_a_list @@ -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 - - basic_stats_heatmap_seeting + - basic_stats_heatmap_seeting - Plot all color maps to view by right click **Theme** - ![right_click_theme](MetaX_Cookbook.assets/right_click_theme.png) - - all_cmap + - all_cmap - **Plot:** - heatmap_original + heatmap_original - **Modify** the pic to fit the window to get the **Perfect picture**: - modify_pic + modify_pic - - heatmap_fixed + - heatmap_fixed @@ -434,22 +435,22 @@ We can select **meta** **groups** or **samples** (default a - **Bar Plot:** -basic_stats_bar +basic_stats_bar - **interactive function:** - basic_stats_bar_setting + basic_stats_bar_setting - change to line plot: - basic_stats_bar_to_line + basic_stats_bar_to_line - 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) - - basic_stats_bar_3d + - basic_stats_bar_3d @@ -457,7 +458,7 @@ We can select **meta** **groups** or **samples** (default a - Query everything of a peptide - peptide_query + peptide_query @@ -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**] -t_test +t_test ### ANOVA-TEST - select some groups or all groups to ANOVA Test for **[Taxa, Function, Taxa-Func and Peptide table**] -anova_test +anova_test ### 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 - t_test_res + t_test_res @@ -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** -corss_heatmap_setting +corss_heatmap_setting - Taxa-Func cross heatmap: - The orange cells mean in the corresponding function ( X-axis) and Taxa( Y-axis) are significantly different between groups. -corss_heatmap +corss_heatmap - Func(Taxa) Heatmap: - The colour shows the intensity of the significant Func(Taxa) between groups. - t_test_heatmap + t_test_heatmap - Significant Taxa-Func Heatmap: @@ -520,7 +521,7 @@ We can select **meta** **groups** or **samples** (default a ### TUKEY_TEST -tukey_test +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. - taxa_func_linked_only + taxa_func_linked_only - 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 -tukey_plot +tukey_plot ### 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 - - dunnetts_heatmap + - dunnetts_heatmap @@ -572,7 +573,7 @@ We can select **meta** **groups** or **samples** (default a -image-20230728123725717 +image-20230728123725717 - Select p-adjust, log2FC to plot @@ -580,19 +581,19 @@ We can select **meta** **groups** or **samples** (default a - Volcano: - volcano + volcano - Sankey: - The last node level is the functions linked to each Taxon (When plotting Taxa-Func) - taxa_func_sankey + taxa_func_sankey ### Co-Expression Networks - select Groups or Samples to calculate the correlation and plot the network -image-20230728142606826 +image-20230728142606826 - 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) - image-20230728143058568 + image-20230728143058568 - 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 -co_network_pic +co_network_pic @@ -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 -image-20230728143806833 +image-20230728143806833 - Clusters plot (clustered by **k-means**) - The coloured line is the average - image-20230728144230514 + image-20230728144230514 @@ -632,7 +633,7 @@ We can select **meta** **groups** or **samples** (default a - The dashed red line is the average - image-20240304120503032 + image-20240304120503032 @@ -644,7 +645,7 @@ We can select **meta** **groups** or **samples** (default a ### Taxa-Func Link Plot -image-20230728150309898 +image-20230728150309898 - 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 - image-20230728152236517 + image-20230728152236517 - 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** - image-20230728152953911 + image-20230728152953911 -image-20230728151451213 +image-20230728151451213 - Plot **peptides** in one Function of a Taxon - taxa_func_link_pep_heatmap + taxa_func_link_pep_heatmap - taxa_func_link_pep_bar + taxa_func_link_pep_bar - Switch Bar to Stacked or not ( Line) - bar_switch_satck + bar_switch_satck - Change Bar plot to Lines - bar_to_line + bar_to_line ### Taxa-Func Network - Select some groups or samples (default all) - add some taxa, func or taxa-func to focus the window (Optional) - image-20230728145518517 + image-20230728145518517 - 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 - taxa_func_network + taxa_func_network @@ -719,7 +720,7 @@ We can select **meta** **groups** or **samples** (default a - **Show or Hide the Console** - - show_console + - show_console - **Any Table Mode**