From 93d94c06e304960c60bbbbdd6271acd0e2505c12 Mon Sep 17 00:00:00 2001 From: "Lea@Mac" Date: Thu, 4 Jul 2024 10:24:08 +0200 Subject: [PATCH] sample correlation docs done --- docs/_site/assets/js/search-data.json | 38 +++++++++++------ docs/_site/code-and-data.html | 2 +- docs/_site/code-and-data/data.html | 2 +- docs/_site/code-and-data/examples.html | 2 +- docs/_site/code-and-data/r-code.html | 2 +- docs/_site/faq.html | 2 +- docs/_site/index.html | 2 +- docs/_site/installation.html | 2 +- docs/_site/interface-details.html | 2 +- .../enrichment-analysis.html | 2 +- docs/_site/interface-details/heatmap.html | 2 +- docs/_site/interface-details/pca.html | 2 +- .../interface-details/pre-processing.html | 2 +- .../required-data-input.html | 2 +- .../interface-details/sample-correlation.html | 2 +- docs/_site/interface-details/selection.html | 2 +- .../significance-analysis.html | 2 +- .../single-gene-visualisations.html | 2 +- docs/_site/showcases.html | 2 +- docs/_site/showcases/showcase-a.html | 2 +- docs/_site/showcases/showcase-b.html | 2 +- docs/_site/welcome.html | 2 +- docs/interface-details/sample-correlation.md | 42 +++++++++++++++++-- 23 files changed, 86 insertions(+), 36 deletions(-) diff --git a/docs/_site/assets/js/search-data.json b/docs/_site/assets/js/search-data.json index c13f7ebf..02989a10 100644 --- a/docs/_site/assets/js/search-data.json +++ b/docs/_site/assets/js/search-data.json @@ -202,76 +202,90 @@ "relUrl": "/interface-details/required-data-input.html" },"29": { - "doc": "Sample correlation", - "title": "Sample correlation", - "content": " ", + "doc": "Sample Correlation", + "title": "Sample Correlation", + "content": "The Sample Correlation tab is divided into two main sections: the side panel and the main panel. ", "url": "/OmicShiny/interface-details/sample-correlation.html", "relUrl": "/interface-details/sample-correlation.html" },"30": { + "doc": "Sample Correlation", + "title": "Side Panel", + "content": "In the side panel, you have the following options: . | Choose the correlation method: You can select from Pearson, Spearman, or Kendall correlation methods. | Understanding Correlation Methods provides a detailed explanation of each method. | When to use: . | Pearson: Use this when you assume a linear relationship between your variables and both variables are normally distributed. | Spearman: Use this when your data is not normally distributed or you have ordinal variables. | Kendall: Use this when you have small sample sizes or need to handle ties in your data. | . | . | Get Sample Correlation: Clicking this button will generate the heatmap in the main panel based on the selected correlation method. | Choose the color annotation for the samples: Below the horizontal line, you can choose different options to color the rows. These options come from the sample annotations provided initially. This can help to potentially explain clustering behavior observed in the heatmap. More details on these options can be found under Required Data Input or Showcase A. | . ", + "url": "/OmicShiny/interface-details/sample-correlation.html#side-panel", + + "relUrl": "/interface-details/sample-correlation.html#side-panel" + },"31": { + "doc": "Sample Correlation", + "title": "Main Panel", + "content": "The main panel displays the correlation heatmap. Here are some key points: . | Information Display: At the top of the main panel, some information is displayed regarding the computation of the correlation matrix. | Heatmap Visualization: The heatmap provides a visual representation of the sample correlation based on the selected method and coloring option. | Download Options: The visualization can be downloaded directly in common formats (e.g., PNG, TIFF, PDF) or sent to the report. You can also download the underlying R code and data. For more information, check out Interface Details. | Non-Interactive Plot: Note that this plot is not interactive. | . Other Notes . | Question Marks: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! | Clustering Behavior: Observing the clustering in the heatmap can give insights into the relationships between different samples based on the selected annotation. | . ", + "url": "/OmicShiny/interface-details/sample-correlation.html#main-panel", + + "relUrl": "/interface-details/sample-correlation.html#main-panel" + },"32": { "doc": "Data Selection", "title": "Data Selection", "content": " ", "url": "/OmicShiny/interface-details/selection.html", "relUrl": "/interface-details/selection.html" - },"31": { + },"33": { "doc": "Showcase A", "title": "Showcase A", "content": "Details about Showcase A. ", "url": "/OmicShiny/showcases/showcase-a.html", "relUrl": "/showcases/showcase-a.html" - },"32": { + },"34": { "doc": "Showcase A", "title": "Showcase B", "content": "Details about Showcase B. ", "url": "/OmicShiny/showcases/showcase-b.html#showcase-b", "relUrl": "/showcases/showcase-b.html#showcase-b" - },"33": { + },"35": { "doc": "Showcase A", "title": "Showcase A", "content": " ", "url": "/OmicShiny/showcases/showcase-b.html", "relUrl": "/showcases/showcase-b.html" - },"34": { + },"36": { "doc": "Showcases", "title": "Showcases Overview", "content": "In this section, you will find two showcases, each utilizing different datasets to illustrate various features and functionalities of the App. | Data Input Showcase: This example demonstrates how to work with data inputs, emphasizing different aspects of data manipulation within the App. | . => Go to the Showcase A . | Rearrange results and Specialized Analysis: This showcase highlights how to summarize produced results in a publication-like manner and further expand upon them with specialized analyses. | . => Go to the Showcase B test . ", "url": "/OmicShiny/showcases.html#showcases-overview", "relUrl": "/showcases.html#showcases-overview" - },"35": { + },"37": { "doc": "Showcases", "title": "Showcases", "content": " ", "url": "/OmicShiny/showcases.html", "relUrl": "/showcases.html" - },"36": { + },"38": { "doc": "Significance Analysis", "title": "Significance Analysis", "content": " ", "url": "/OmicShiny/interface-details/significance-analysis.html", "relUrl": "/interface-details/significance-analysis.html" - },"37": { + },"39": { "doc": "Single Gene Visualisations", "title": "Single Gene Visualisations", "content": " ", "url": "/OmicShiny/interface-details/single-gene-visualisations.html", "relUrl": "/interface-details/single-gene-visualisations.html" - },"38": { + },"40": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsArt Documentation 🎨", "content": "Image generated using DALL-E by OpenAI. Adjusted by Lea Seep . If you are looking for the web app, please visit: 🌐 cOmicsART Web App . Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section. Have fun exploring! πŸŽ‰ . Quick Links to Get You Started: . | πŸ“š Want to know the required data and format? Visit Interface Details. | πŸ”§ Need to run the app locally? Check out the Installation Guide. | πŸ’‘ Looking for customization inspiration? Explore our Customization Examples. | πŸ“Š Want to know more about the significance analysis? Visit Significance Analysis | . ", "url": "/OmicShiny/welcome.html#welcome-to--comicsart-documentation-", "relUrl": "/welcome.html#welcome-to--comicsart-documentation-" - },"39": { + },"41": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsART", "content": " ", diff --git a/docs/_site/code-and-data.html b/docs/_site/code-and-data.html index c8f3e296..103e9d1c 100644 --- a/docs/_site/code-and-data.html +++ b/docs/_site/code-and-data.html @@ -1 +1 @@ - Code and Data download | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Table of contents

+ Code and Data download | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Table of contents

diff --git a/docs/_site/code-and-data/data.html b/docs/_site/code-and-data/data.html index 18995560..83c59d94 100644 --- a/docs/_site/code-and-data/data.html +++ b/docs/_site/code-and-data/data.html @@ -1 +1 @@ - Data object | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Data object | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/code-and-data/examples.html b/docs/_site/code-and-data/examples.html index 9435addf..7dcaa9fa 100644 --- a/docs/_site/code-and-data/examples.html +++ b/docs/_site/code-and-data/examples.html @@ -1 +1 @@ - Examples | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Examples | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/code-and-data/r-code.html b/docs/_site/code-and-data/r-code.html index a3318bb9..ae8f8e6d 100644 --- a/docs/_site/code-and-data/r-code.html +++ b/docs/_site/code-and-data/r-code.html @@ -1 +1 @@ - R code | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ R code | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/faq.html b/docs/_site/faq.html index bbb9881d..1c26b428 100644 --- a/docs/_site/faq.html +++ b/docs/_site/faq.html @@ -1 +1 @@ - FAQ | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Frequently Asked Questions (FAQ)

1. What is ComicsART?
ComicsART is a tool designed to facilitate easy explorative and statistical analysis. It stands for customizable Omics Analysis and Reporting Tool. Its special focus is to guarantee reproducibility within the GUI providing you an autogenerated HTML report of which clicks have been done and to guarantee reprodubility without the GUI provding on click all code and data to fully reproduce in R what you have done within the GUI - allowing then for to enjoy the freedom and options programming gives you!
2. How do I get started with ComicsART?
There are several ways- depending on what type of learner you are! You might want to first read our publication that includes the whole picture and our vision. If you want to experience the app without the own data you can use the test-dataset by simply selecting Testdata tab in the sidebar and then starting your journey. We have also screen recordings available on YouTube as well as this extensive documentation you already found! In case you are left with question feel free to mail us: cOmicsArtist@outlook.de.
3. My Data upload does not work - what do I do?
ComicsART is designed to work with .csv files. If you are experiencing issues with the data upload, please ensure that your file is in the correct format. cOmicsART also provides a test dataset that you can use to familiarize yourself with the data-format the tool is expecting (Click within the Data Selection Main tab on 'Download example data'). Moreover, you can upload your data and click "Inspect Data" **before** clicking 'Upload new data'. Here, we try everything to still upload your data and run through our tests. At the bottom you can see which test fails and hinting you what you might have done wrong. Common issues are: Not exactly the same row or columnnames, missing values, wrong delimiters (watch out if you use german excel with ',' being the decimal sign), invalid names involving commas, whitespaces and 'Umlaute' (Γ€,ΓΆ,ΓΌ). If you are still experiencing issues, please contact our support team for assistance.
4. The app is running since ages and nothing happens
Is grey overlay visibile? If yes, tha app backend has crashed - this can have multiple reasons. It could be a disconnection between your browser and the server or the server itself is not running anymore. If you refresh the page you might be able to reconnect but potentially have to redo your work. We try to almost alsways give you the option to still recieve the HTML report so you know at least what has been done up to this point. If this happens often to you it might be a good idea to employ our DOCKER image or install the app locally on your machine. Instructions can be found in the 'Installation' tab in the sidebar.
+ FAQ | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
This site uses Just the Docs, a documentation theme for Jekyll.

Frequently Asked Questions (FAQ)

1. What is ComicsART?
ComicsART is a tool designed to facilitate easy explorative and statistical analysis. It stands for customizable Omics Analysis and Reporting Tool. Its special focus is to guarantee reproducibility within the GUI providing you an autogenerated HTML report of which clicks have been done and to guarantee reprodubility without the GUI provding on click all code and data to fully reproduce in R what you have done within the GUI - allowing then for to enjoy the freedom and options programming gives you!
2. How do I get started with ComicsART?
There are several ways- depending on what type of learner you are! You might want to first read our publication that includes the whole picture and our vision. If you want to experience the app without the own data you can use the test-dataset by simply selecting Testdata tab in the sidebar and then starting your journey. We have also screen recordings available on YouTube as well as this extensive documentation you already found! In case you are left with question feel free to mail us: cOmicsArtist@outlook.de.
3. My Data upload does not work - what do I do?
ComicsART is designed to work with .csv files. If you are experiencing issues with the data upload, please ensure that your file is in the correct format. cOmicsART also provides a test dataset that you can use to familiarize yourself with the data-format the tool is expecting (Click within the Data Selection Main tab on 'Download example data'). Moreover, you can upload your data and click "Inspect Data" **before** clicking 'Upload new data'. Here, we try everything to still upload your data and run through our tests. At the bottom you can see which test fails and hinting you what you might have done wrong. Common issues are: Not exactly the same row or columnnames, missing values, wrong delimiters (watch out if you use german excel with ',' being the decimal sign), invalid names involving commas, whitespaces and 'Umlaute' (Γ€,ΓΆ,ΓΌ). If you are still experiencing issues, please contact our support team for assistance.
4. The app is running since ages and nothing happens
Is grey overlay visibile? If yes, tha app backend has crashed - this can have multiple reasons. It could be a disconnection between your browser and the server or the server itself is not running anymore. If you refresh the page you might be able to reconnect but potentially have to redo your work. We try to almost alsways give you the option to still recieve the HTML report so you know at least what has been done up to this point. If this happens often to you it might be a good idea to employ our DOCKER image or install the app locally on your machine. Instructions can be found in the 'Installation' tab in the sidebar.
diff --git a/docs/_site/index.html b/docs/_site/index.html index 33eb4a23..fb2adcaf 100644 --- a/docs/_site/index.html +++ b/docs/_site/index.html @@ -1 +1 @@ - Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Welcome to cOmicsArt Documentation 🎨

A comic about a cat finding cOmicsART Image generated using DALL-E by OpenAI. Adjusted by Lea Seep

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

+ Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
This site uses Just the Docs, a documentation theme for Jekyll.

Welcome to cOmicsArt Documentation 🎨

A comic about a cat finding cOmicsART Image generated using DALL-E by OpenAI. Adjusted by Lea Seep

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

diff --git a/docs/_site/installation.html b/docs/_site/installation.html index 343fd71e..73197ea8 100644 --- a/docs/_site/installation.html +++ b/docs/_site/installation.html @@ -1 +1 @@ - Local Installation | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Introduction

Why do you want to install cOmicsART locally? If you just want to use it make sure to checkout the website: cOmicsART. For this there is no installation effort required. If you know you are right here, let’s get started.

Running a cOmicsART Using Docker

This guide will help you use the provided Docker image to start your Shiny app.

Prerequisites

  1. Install Docker: Ensure Docker is installed on your system. You can download and install Docker from Docker’s official website.

Steps to Run the ShinyApp

…..

Local deploy the App from github

….

+ Local Installation | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Introduction

Why do you want to install cOmicsART locally? If you just want to use it make sure to checkout the website: cOmicsART. For this there is no installation effort required. If you know you are right here, let’s get started.

Running a cOmicsART Using Docker

This guide will help you use the provided Docker image to start your Shiny app.

Prerequisites

  1. Install Docker: Ensure Docker is installed on your system. You can download and install Docker from Docker’s official website.

Steps to Run the ShinyApp

…..

Local deploy the App from github

….

diff --git a/docs/_site/interface-details.html b/docs/_site/interface-details.html index bb82761c..aefff8ae 100644 --- a/docs/_site/interface-details.html +++ b/docs/_site/interface-details.html @@ -1 +1 @@ - Interface Details | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Interface Details

If you need tab-specific information, navigate to the respective documentation using the left sidebar.

General Design Characteristics

User Interface and Analysis Features

The cOmicsART user interface evolves gradually to guide users through the necessary steps:

  • πŸ“₯ Data Input Tab: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab.
  • βš™οΈ Pre-Processing Tab: This tab becomes accessible after a successful data upload. It offers multiple options to prepare the data for analysis, including diagnostic plots to check for normal distribution.
  • πŸ“ˆ Analysis Tabs: Six analysis options are available, each in its own tab. These tabs provide interactive result visualizations and various analytical functions.

To get more information on the tabs, navigate to the respective documentation using the left sidebar.

  • πŸ–±οΈ Button Clicks: Used to evoke actions.
  • ⏳ Loading Bars: Display waiting times during processing.
  • ❓ Question Marks: Provide quick help and guide to respective detailed documentation found on this very site.
  • πŸ”½ Dropdown Menus: Offer options for selection. Sometimes multiple items can be selected. If clicking on a selected item it is removed from the selection.
  • β˜‘οΈ Checkboxes: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated.
  • πŸ“ Sliding Bars: Used to adjust numeric parameters or ranges. The range of the sliding bar is displayed above the bar. Simply slide the bar to the desired value.
  • πŸ“ Text Fields: Used to enter text. Within cOmicsART these fields are mostly used to hold your Notes, which are saved in the HTML report at the appropriate position. You can use markdown syntax here.

Features Across Tabs

  1. Side Panel Structure: Each tab, except the input tab, has a side panel divided by a horizontal line:
    • Upper Section: Contains options affecting the analysis, requiring recomputation when changed. The analysis is triggered by a "Do/Get analysis" button above the division line.
    • Lower Section: Displays secondary parameters with changes reflecting immediately in the results (automatic update).
  2. Main Panel Structure: Each main panel contains the visualization of the analysis results. Some panels are further subdivided to show multiple results, for example, the Significance Analysis tab.
  3. Picture Download Options: Users can download visualizations and results in common formats (e.g., PNG, TIFF, PDF). There are respective buttons to select the file format. Upon 'Save plot' the file is downloaded to the local machine.
  4. Sending Visualizations to Report: Upon button click on 'Send only to report' the current shown visualization and associated parameters are saved to the Report. Hence, you can play around with parameters and can save the one of interest to you without cluttering the report with all tried options.
  5. Get Underlying R Code and Data: Upon button click, the R script and respective data to generate shown plot will be presented for download. The script includes the Data selection, pre-processing as well as the respective analysis. For more details make sure to check out [Code and Data](/OmicShiny/code-and-data.html).
  6. Notes: At the bottom of each tab you can find the Notes field - here you can enter text which will be saved within the report. You can use [markdown syntax](https://www.markdownguide.org/cheat-sheet/) here.
The design of the side panel

Table of contents

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Interface Details

If you need tab-specific information, navigate to the respective documentation using the left sidebar.

General Design Characteristics

User Interface and Analysis Features

The cOmicsART user interface evolves gradually to guide users through the necessary steps:

  • πŸ“₯ Data Input Tab: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab.
  • βš™οΈ Pre-Processing Tab: This tab becomes accessible after a successful data upload. It offers multiple options to prepare the data for analysis, including diagnostic plots to check for normal distribution.
  • πŸ“ˆ Analysis Tabs: Six analysis options are available, each in its own tab. These tabs provide interactive result visualizations and various analytical functions.

To get more information on the tabs, navigate to the respective documentation using the left sidebar.

  • πŸ–±οΈ Button Clicks: Used to evoke actions.
  • ⏳ Loading Bars: Display waiting times during processing.
  • ❓ Question Marks: Provide quick help and guide to respective detailed documentation found on this very site.
  • πŸ”½ Dropdown Menus: Offer options for selection. Sometimes multiple items can be selected. If clicking on a selected item it is removed from the selection.
  • β˜‘οΈ Checkboxes: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated.
  • πŸ“ Sliding Bars: Used to adjust numeric parameters or ranges. The range of the sliding bar is displayed above the bar. Simply slide the bar to the desired value.
  • πŸ“ Text Fields: Used to enter text. Within cOmicsART these fields are mostly used to hold your Notes, which are saved in the HTML report at the appropriate position. You can use markdown syntax here.

Features Across Tabs

  1. Side Panel Structure: Each tab, except the input tab, has a side panel divided by a horizontal line:
    • Upper Section: Contains options affecting the analysis, requiring recomputation when changed. The analysis is triggered by a "Do/Get analysis" button above the division line.
    • Lower Section: Displays secondary parameters with changes reflecting immediately in the results (automatic update).
  2. Main Panel Structure: Each main panel contains the visualization of the analysis results. Some panels are further subdivided to show multiple results, for example, the Significance Analysis tab.
  3. Picture Download Options: Users can download visualizations and results in common formats (e.g., PNG, TIFF, PDF). There are respective buttons to select the file format. Upon 'Save plot' the file is downloaded to the local machine.
  4. Sending Visualizations to Report: Upon button click on 'Send only to report' the current shown visualization and associated parameters are saved to the Report. Hence, you can play around with parameters and can save the one of interest to you without cluttering the report with all tried options.
  5. Get Underlying R Code and Data: Upon button click, the R script and respective data to generate shown plot will be presented for download. The script includes the Data selection, pre-processing as well as the respective analysis. For more details make sure to check out [Code and Data](/OmicShiny/code-and-data.html).
  6. Notes: At the bottom of each tab you can find the Notes field - here you can enter text which will be saved within the report. You can use [markdown syntax](https://www.markdownguide.org/cheat-sheet/) here.
The design of the side panel

Table of contents

diff --git a/docs/_site/interface-details/enrichment-analysis.html b/docs/_site/interface-details/enrichment-analysis.html index 4caa739e..0cda0e6f 100644 --- a/docs/_site/interface-details/enrichment-analysis.html +++ b/docs/_site/interface-details/enrichment-analysis.html @@ -1 +1 @@ - Enrichment Analysis | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Enrichment Analysis | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/interface-details/heatmap.html b/docs/_site/interface-details/heatmap.html index 65059a90..3b9cd682 100644 --- a/docs/_site/interface-details/heatmap.html +++ b/docs/_site/interface-details/heatmap.html @@ -1 +1 @@ - Heatmap | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Heatmap | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/interface-details/pca.html b/docs/_site/interface-details/pca.html index 4eb30339..468fa1af 100644 --- a/docs/_site/interface-details/pca.html +++ b/docs/_site/interface-details/pca.html @@ -1 +1 @@ - PCA | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Principle Component Analysis (PCA)

PCA Background

Reactive options

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Principle Component Analysis (PCA)

PCA Background

Reactive options

diff --git a/docs/_site/interface-details/pre-processing.html b/docs/_site/interface-details/pre-processing.html index 31981148..0dd1f83e 100644 --- a/docs/_site/interface-details/pre-processing.html +++ b/docs/_site/interface-details/pre-processing.html @@ -1 +1 @@ - Pre-processing | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Pre-processing | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/interface-details/required-data-input.html b/docs/_site/interface-details/required-data-input.html index 5ccf5ff3..6ac6b5e9 100644 --- a/docs/_site/interface-details/required-data-input.html +++ b/docs/_site/interface-details/required-data-input.html @@ -1 +1 @@ - Data Input | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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The very start

To start your own analysis, you need to pass the first hurdle - Uploading your data. (Note: If you want to check out what the app is capable of you might want to use the Test data, how to exactly do it check out Interface Details Within cOmicsART you have several options to do so:

  • You have at least a data matrix of your measurements. Then start here
    • a data matrix can be, e.g., a count-table, or measured concentrations for multiple entities and samples. At least means, that you might already have also a sample table and /or a measurement table
  • You have a data matrix and a Metadatasheet
    • a Metadasheet is a handy way to organise not only your data, but also your group’s and beyond developed within the Hasenauer Lab. At the moment the Metadatasheet can be supplied instead of a sample table. We are planning to expand on the connection of the Metadatasheet and cOmicsART - stay tuned.
  • You have a cOmicsART created rds object
    • or you may know what rds objects are and want to create one for your collaboration partners. Check out its required structure

General remarks on data input

cOmicsART expects overall three data tables, which can be supplied in different ways, holding information about the measurement itself as well as information regarding the measured samples and information regarding the measured entities, such as genes, metabolites or lipids. We provide here the description of the minimal requirements, however note that you are not limited to theese. Actually adjusting the data input, esspecially annotation is often part of the explorative phase. Checkout Showcase A for an examples.

Starting with a single table

The measurement table

Creating a Sample table

Creating a annotation table

in short

The files must be in the following format:

  1. data-matrix (.csv)
    • contains the actual data, e.g. counts
    • must have the samples (e.g. mouse 1) in the columns and a unique naming as column name
    • must have the entities (e.g. genes) in the rows and a unique rowname (e.g. ENSEMBL ID)
  2. sample-table (.csv)
    • contains metadata about each sample (e.g. disease status) (To come: combination with the Metadata sheet)
    • must have the same naming as in data-matrix (1.colnames) in the rownames
    • must have at least one column name global_ID, this will be used to refer to the sample (in e.g. Volcano plot) (in future not necassary anymore)
  3. row-annotation (.csv)
    • contains metadata about the biological entities (e.g. if gene is protein coding)
    • must have the same naming as in data-matrix (1.rownames) in the rownames
    • if you do not have any information just add a column with the gene-names

Some pitfalls you may fall into:

  • The files must be uploaded at their respective position (data matrix, sample annotation, entities annotation).
  • The files need to be .csv files, which also means that they need to be comma separated not semicolon separated. When exporting from excel make sure to check that the separator is a comma. If your Excel is in german, your default export uses semicolons which will lead to errors!
  • As stated above, the column names in the data matrix must be the same as the row names in the sample annotation. And the row names in the data matrix must be the same as the row names in the entities annotation. Upon Upload before pressing β€˜Do’ you can switch the tab to go to β€˜Upload for visual inspectionβ€˜. Here, you can inspect the uploaded files and check fi that corresponds to your expectations. Additionally, at the bottom several outputs from test are given - there should be all β€˜Yes’.

Starting with a single table and a Metadatasheet

Starting with a rds-object

[advanced] RDS-Structure

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The very start

To start your own analysis, you need to pass the first hurdle - Uploading your data. (Note: If you want to check out what the app is capable of you might want to use the Test data, how to exactly do it check out Interface Details Within cOmicsART you have several options to do so:

  • You have at least a data matrix of your measurements. Then start here
    • a data matrix can be, e.g., a count-table, or measured concentrations for multiple entities and samples. At least means, that you might already have also a sample table and /or a measurement table
  • You have a data matrix and a Metadatasheet
    • a Metadasheet is a handy way to organise not only your data, but also your group’s and beyond developed within the Hasenauer Lab. At the moment the Metadatasheet can be supplied instead of a sample table. We are planning to expand on the connection of the Metadatasheet and cOmicsART - stay tuned.
  • You have a cOmicsART created rds object
    • or you may know what rds objects are and want to create one for your collaboration partners. Check out its required structure

General remarks on data input

cOmicsART expects overall three data tables, which can be supplied in different ways, holding information about the measurement itself as well as information regarding the measured samples and information regarding the measured entities, such as genes, metabolites or lipids. We provide here the description of the minimal requirements, however note that you are not limited to theese. Actually adjusting the data input, esspecially annotation is often part of the explorative phase. Checkout Showcase A for an examples.

Starting with a single table

The measurement table

Creating a Sample table

Creating a annotation table

in short

The files must be in the following format:

  1. data-matrix (.csv)
    • contains the actual data, e.g. counts
    • must have the samples (e.g. mouse 1) in the columns and a unique naming as column name
    • must have the entities (e.g. genes) in the rows and a unique rowname (e.g. ENSEMBL ID)
  2. sample-table (.csv)
    • contains metadata about each sample (e.g. disease status) (To come: combination with the Metadata sheet)
    • must have the same naming as in data-matrix (1.colnames) in the rownames
    • must have at least one column name global_ID, this will be used to refer to the sample (in e.g. Volcano plot) (in future not necassary anymore)
  3. row-annotation (.csv)
    • contains metadata about the biological entities (e.g. if gene is protein coding)
    • must have the same naming as in data-matrix (1.rownames) in the rownames
    • if you do not have any information just add a column with the gene-names

Some pitfalls you may fall into:

  • The files must be uploaded at their respective position (data matrix, sample annotation, entities annotation).
  • The files need to be .csv files, which also means that they need to be comma separated not semicolon separated. When exporting from excel make sure to check that the separator is a comma. If your Excel is in german, your default export uses semicolons which will lead to errors!
  • As stated above, the column names in the data matrix must be the same as the row names in the sample annotation. And the row names in the data matrix must be the same as the row names in the entities annotation. Upon Upload before pressing β€˜Do’ you can switch the tab to go to β€˜Upload for visual inspectionβ€˜. Here, you can inspect the uploaded files and check fi that corresponds to your expectations. Additionally, at the bottom several outputs from test are given - there should be all β€˜Yes’.

Starting with a single table and a Metadatasheet

Starting with a rds-object

[advanced] RDS-Structure

diff --git a/docs/_site/interface-details/sample-correlation.html b/docs/_site/interface-details/sample-correlation.html index 4596cde3..bda7dcfe 100644 --- a/docs/_site/interface-details/sample-correlation.html +++ b/docs/_site/interface-details/sample-correlation.html @@ -1 +1 @@ - Sample correlation | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Sample Correlation | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Sample Correlation

The Sample Correlation tab is divided into two main sections: the side panel and the main panel.

Side Panel

In the side panel, you have the following options:

  • Choose the correlation method: You can select from Pearson, Spearman, or Kendall correlation methods.
    • Understanding Correlation Methods provides a detailed explanation of each method.
    • When to use:
      • Pearson: Use this when you assume a linear relationship between your variables and both variables are normally distributed.
      • Spearman: Use this when your data is not normally distributed or you have ordinal variables.
      • Kendall: Use this when you have small sample sizes or need to handle ties in your data.

  • Get Sample Correlation: Clicking this button will generate the heatmap in the main panel based on the selected correlation method.

  • Choose the color annotation for the samples: Below the horizontal line, you can choose different options to color the rows. These options come from the sample annotations provided initially. This can help to potentially explain clustering behavior observed in the heatmap.

    More details on these options can be found under Required Data Input or Showcase A.

Main Panel

The main panel displays the correlation heatmap. Here are some key points:

  • Information Display: At the top of the main panel, some information is displayed regarding the computation of the correlation matrix.
  • Heatmap Visualization: The heatmap provides a visual representation of the sample correlation based on the selected method and coloring option.
  • Download Options: The visualization can be downloaded directly in common formats (e.g., PNG, TIFF, PDF) or sent to the report. You can also download the underlying R code and data. For more information, check out Interface Details.
  • Non-Interactive Plot: Note that this plot is not interactive.

Other Notes

  • Question Marks: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped!
  • Clustering Behavior: Observing the clustering in the heatmap can give insights into the relationships between different samples based on the selected annotation.
diff --git a/docs/_site/interface-details/selection.html b/docs/_site/interface-details/selection.html index 90e1883f..96091ff5 100644 --- a/docs/_site/interface-details/selection.html +++ b/docs/_site/interface-details/selection.html @@ -1 +1 @@ - Data Selection | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Data Selection

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Data Selection

diff --git a/docs/_site/interface-details/significance-analysis.html b/docs/_site/interface-details/significance-analysis.html index 5a3265cf..c125afac 100644 --- a/docs/_site/interface-details/significance-analysis.html +++ b/docs/_site/interface-details/significance-analysis.html @@ -1 +1 @@ - Significance Analysis | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Significance Analysis | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/interface-details/single-gene-visualisations.html b/docs/_site/interface-details/single-gene-visualisations.html index 71c43334..debf182d 100644 --- a/docs/_site/interface-details/single-gene-visualisations.html +++ b/docs/_site/interface-details/single-gene-visualisations.html @@ -1 +1 @@ - Single Gene Visualisations | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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+ Single Gene Visualisations | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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diff --git a/docs/_site/showcases.html b/docs/_site/showcases.html index e8e15498..0c47ea5f 100644 --- a/docs/_site/showcases.html +++ b/docs/_site/showcases.html @@ -1 +1 @@ - Showcases | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Showcases Overview

In this section, you will find two showcases, each utilizing different datasets to illustrate various features and functionalities of the App.

  1. Data Input Showcase: This example demonstrates how to work with data inputs, emphasizing different aspects of data manipulation within the App.

=> Go to the Showcase A

  1. Rearrange results and Specialized Analysis: This showcase highlights how to summarize produced results in a publication-like manner and further expand upon them with specialized analyses.

=> Go to the Showcase B test

Table of contents

+ Showcases | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
This site uses Just the Docs, a documentation theme for Jekyll.

Showcases Overview

In this section, you will find two showcases, each utilizing different datasets to illustrate various features and functionalities of the App.

  1. Data Input Showcase: This example demonstrates how to work with data inputs, emphasizing different aspects of data manipulation within the App.

=> Go to the Showcase A

  1. Rearrange results and Specialized Analysis: This showcase highlights how to summarize produced results in a publication-like manner and further expand upon them with specialized analyses.

=> Go to the Showcase B test

Table of contents

diff --git a/docs/_site/showcases/showcase-a.html b/docs/_site/showcases/showcase-a.html index b93a93a7..97646761 100644 --- a/docs/_site/showcases/showcase-a.html +++ b/docs/_site/showcases/showcase-a.html @@ -1 +1 @@ - Showcase A | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Showcase A

Details about Showcase A.

+ Showcase A | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Showcase A

Details about Showcase A.

diff --git a/docs/_site/showcases/showcase-b.html b/docs/_site/showcases/showcase-b.html index 61c46268..a0ecbfd9 100644 --- a/docs/_site/showcases/showcase-b.html +++ b/docs/_site/showcases/showcase-b.html @@ -1 +1 @@ - Showcase A | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Showcase B

Details about Showcase B.

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Showcase B

Details about Showcase B.

diff --git a/docs/_site/welcome.html b/docs/_site/welcome.html index 671367e3..f6f10e75 100644 --- a/docs/_site/welcome.html +++ b/docs/_site/welcome.html @@ -1 +1 @@ - Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
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Welcome to cOmicsArt Documentation 🎨

A comic about a cat finding cOmicsART Image generated using DALL-E by OpenAI. Adjusted by Lea Seep

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

+ Welcome to cOmicsART | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
This site uses Just the Docs, a documentation theme for Jekyll.

Welcome to cOmicsArt Documentation 🎨

A comic about a cat finding cOmicsART Image generated using DALL-E by OpenAI. Adjusted by Lea Seep

If you are looking for the web app, please visit: 🌐 cOmicsART Web App

Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. πŸ” It can search through the entire documentation and guide you to the relevant section.

Have fun exploring! πŸŽ‰

diff --git a/docs/interface-details/sample-correlation.md b/docs/interface-details/sample-correlation.md index 4f75e890..5735efd0 100644 --- a/docs/interface-details/sample-correlation.md +++ b/docs/interface-details/sample-correlation.md @@ -1,6 +1,42 @@ --- -title: "Sample correlation" +title: "Sample Correlation" layout: default -parent: Interface Details +parent: "Interface Details" nav_order: 3 ---- \ No newline at end of file +--- + +# Sample Correlation + +The Sample Correlation tab is divided into two main sections: the side panel and the main panel. + +## Side Panel + +In the side panel, you have the following options: + +- **Choose the correlation method**: You can select from Pearson, Spearman, or Kendall correlation methods. + - [Understanding Correlation Methods](https://ademos.people.uic.edu/Chapter22.html) provides a detailed explanation of each method. + - **When to use:** + - **Pearson**: Use this when you assume a linear relationship between your variables and both variables are normally distributed. + - **Spearman**: Use this when your data is not normally distributed or you have ordinal variables. + - **Kendall**: Use this when you have small sample sizes or need to handle ties in your data. + +- **Get Sample Correlation**: Clicking this button will generate the heatmap in the main panel based on the selected correlation method. + +- **Choose the color annotation for the samples**: Below the horizontal line, you can choose different options to color the rows. These options come from the sample annotations provided initially. This can help to potentially explain clustering behavior observed in the heatmap. + + More details on these options can be found under [Required Data Input](required-data-input.md) or [Showcase A](../showcases/showcase-a.md). + +## Main Panel + +The main panel displays the correlation heatmap. Here are some key points: + +- **Information Display**: At the top of the main panel, some information is displayed regarding the computation of the correlation matrix. +- **Heatmap Visualization**: The heatmap provides a visual representation of the sample correlation based on the selected method and coloring option. +- **Download Options**: The visualization can be downloaded directly in common formats (e.g., PNG, TIFF, PDF) or sent to the report. You can also download the underlying R code and data. For more information, check out [Interface Details](interface-details.md). +- **Non-Interactive Plot**: Note that this plot is not interactive. + +### Other Notes + +- **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! +- **Clustering Behavior**: Observing the clustering in the heatmap can give insights into the relationships between different samples based on the selected annotation. +