diff --git a/docs/_site/assets/css/just-the-docs-dark.css b/docs/_site/assets/css/just-the-docs-dark.css index 20f958fa..e8e2e76b 100644 --- a/docs/_site/assets/css/just-the-docs-dark.css +++ b/docs/_site/assets/css/just-the-docs-dark.css @@ -435,7 +435,7 @@ blockquote { margin: 10px 0; margin-block-start: 0; margin-inline-start: 0; padd @media (min-width: 31.25rem) { .site-title { font-size: 1.5rem !important; line-height: 1.25; } } @media (min-width: 50rem) { .site-title { padding-top: 0.5rem; padding-bottom: 0.5rem; } } -.site-logo { width: 100%; height: 100%; background-image: url("/assets/images/Logo_cOmicsArt.svg"); background-repeat: no-repeat; background-position: left center; background-size: contain; } +.site-logo { width: 100%; height: 100%; background-image: url("/OmicShiny/assets/images/Logo_cOmicsArt.svg"); background-repeat: no-repeat; background-position: left center; background-size: contain; } .site-button { display: flex; height: 100%; padding: 1rem; align-items: center; } diff --git a/docs/_site/assets/css/just-the-docs-default.css b/docs/_site/assets/css/just-the-docs-default.css index 1c230582..47d655d3 100644 --- a/docs/_site/assets/css/just-the-docs-default.css +++ b/docs/_site/assets/css/just-the-docs-default.css @@ -307,7 +307,7 @@ blockquote { margin: 10px 0; margin-block-start: 0; margin-inline-start: 0; padd @media (min-width: 31.25rem) { .site-title { font-size: 1.5rem !important; line-height: 1.25; } } @media (min-width: 50rem) { .site-title { padding-top: 0.5rem; padding-bottom: 0.5rem; } } -.site-logo { width: 100%; height: 100%; background-image: url("/assets/images/Logo_cOmicsArt.svg"); background-repeat: no-repeat; background-position: left center; background-size: contain; } +.site-logo { width: 100%; height: 100%; background-image: url("/OmicShiny/assets/images/Logo_cOmicsArt.svg"); background-repeat: no-repeat; background-position: left center; background-size: contain; } .site-button { display: flex; height: 100%; padding: 1rem; align-items: center; } diff --git a/docs/_site/assets/css/just-the-docs-light.css b/docs/_site/assets/css/just-the-docs-light.css index 1c230582..47d655d3 100644 --- a/docs/_site/assets/css/just-the-docs-light.css +++ b/docs/_site/assets/css/just-the-docs-light.css @@ -307,7 +307,7 @@ blockquote { margin: 10px 0; margin-block-start: 0; margin-inline-start: 0; padd @media (min-width: 31.25rem) { .site-title { font-size: 1.5rem !important; line-height: 1.25; } } @media (min-width: 50rem) { .site-title { padding-top: 0.5rem; padding-bottom: 0.5rem; } } -.site-logo { width: 100%; height: 100%; background-image: url("/assets/images/Logo_cOmicsArt.svg"); background-repeat: no-repeat; background-position: left center; background-size: contain; } +.site-logo { width: 100%; height: 100%; background-image: url("/OmicShiny/assets/images/Logo_cOmicsArt.svg"); background-repeat: no-repeat; background-position: left center; background-size: contain; } .site-button { display: flex; height: 100%; padding: 1rem; align-items: center; } diff --git a/docs/_site/assets/js/just-the-docs.js b/docs/_site/assets/js/just-the-docs.js index fa70ae50..c8160b66 100644 --- a/docs/_site/assets/js/just-the-docs.js +++ b/docs/_site/assets/js/just-the-docs.js @@ -77,7 +77,7 @@ function disableHeadStyleSheets() { function initSearch() { var request = new XMLHttpRequest(); - request.open('GET', '/assets/js/search-data.json', true); + request.open('GET', '/OmicShiny/assets/js/search-data.json', true); request.onload = function(){ if (request.status >= 200 && request.status < 400) { @@ -456,7 +456,7 @@ jtd.getTheme = function() { jtd.setTheme = function(theme) { var cssFile = document.querySelector('[rel="stylesheet"]'); - cssFile.setAttribute('href', '/assets/css/just-the-docs-' + theme + '.css'); + cssFile.setAttribute('href', '/OmicShiny/assets/css/just-the-docs-' + theme + '.css'); } // Note: pathname can have a trailing slash on a local jekyll server diff --git a/docs/_site/assets/js/search-data.json b/docs/_site/assets/js/search-data.json index 8d6bc105..c13f7ebf 100644 --- a/docs/_site/assets/js/search-data.json +++ b/docs/_site/assets/js/search-data.json @@ -2,280 +2,280 @@ "doc": "Code and Data download", "title": "Code and Data download", "content": " ", - "url": "/code-and-data.html", + "url": "/OmicShiny/code-and-data.html", "relUrl": "/code-and-data.html" },"1": { "doc": "Data object", "title": "Data object", "content": " ", - "url": "/code-and-data/data.html", + "url": "/OmicShiny/code-and-data/data.html", "relUrl": "/code-and-data/data.html" },"2": { "doc": "Enrichment Analysis", "title": "Enrichment Analysis", "content": " ", - "url": "/interface-details/enrichment-analysis.html", + "url": "/OmicShiny/interface-details/enrichment-analysis.html", "relUrl": "/interface-details/enrichment-analysis.html" },"3": { "doc": "Examples", "title": "Examples", "content": " ", - "url": "/code-and-data/examples.html", + "url": "/OmicShiny/code-and-data/examples.html", "relUrl": "/code-and-data/examples.html" },"4": { "doc": "FAQ", "title": "Frequently Asked Questions (FAQ)", "content": "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. ", - "url": "/faq.html#frequently-asked-questions-faq", + "url": "/OmicShiny/faq.html#frequently-asked-questions-faq", "relUrl": "/faq.html#frequently-asked-questions-faq" },"5": { "doc": "FAQ", "title": "FAQ", "content": " ", - "url": "/faq.html", + "url": "/OmicShiny/faq.html", "relUrl": "/faq.html" },"6": { "doc": "Heatmap", "title": "Heatmap", "content": " ", - "url": "/interface-details/heatmap.html", + "url": "/OmicShiny/interface-details/heatmap.html", "relUrl": "/interface-details/heatmap.html" },"7": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsArt Documentation 🎨", - "content": ". 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": "/#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-to----comicsart-documentation-", "relUrl": "/#welcome-to----comicsart-documentation-" },"8": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsART", "content": " ", - "url": "/", + "url": "/OmicShiny/", "relUrl": "/" },"9": { "doc": "Local Installation", "title": "Introduction", "content": "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. ", - "url": "/installation.html#introduction", + "url": "/OmicShiny/installation.html#introduction", "relUrl": "/installation.html#introduction" },"10": { "doc": "Local Installation", "title": "Running a cOmicsART Using Docker", "content": "This guide will help you use the provided Docker image to start your Shiny app. ", - "url": "/installation.html#running-a-comicsart-using-docker", + "url": "/OmicShiny/installation.html#running-a-comicsart-using-docker", "relUrl": "/installation.html#running-a-comicsart-using-docker" },"11": { "doc": "Local Installation", "title": "Prerequisites", "content": ". | Install Docker: Ensure Docker is installed on your system. You can download and install Docker from Docker’s official website. | . ", - "url": "/installation.html#prerequisites", + "url": "/OmicShiny/installation.html#prerequisites", "relUrl": "/installation.html#prerequisites" },"12": { "doc": "Local Installation", "title": "Steps to Run the ShinyApp", "content": "….. ", - "url": "/installation.html#steps-to-run-the-shinyapp", + "url": "/OmicShiny/installation.html#steps-to-run-the-shinyapp", "relUrl": "/installation.html#steps-to-run-the-shinyapp" },"13": { "doc": "Local Installation", "title": "Local deploy the App from github", "content": "…. ", - "url": "/installation.html#local-deploy-the-app-from-github", + "url": "/OmicShiny/installation.html#local-deploy-the-app-from-github", "relUrl": "/installation.html#local-deploy-the-app-from-github" },"14": { "doc": "Local Installation", "title": "Local Installation", "content": " ", - "url": "/installation.html", + "url": "/OmicShiny/installation.html", "relUrl": "/installation.html" },"15": { "doc": "Interface Details", "title": "Interface Details", "content": "If you need tab-specific information, navigate to the respective documentation using the left sidebar. ", - "url": "/interface-details.html", + "url": "/OmicShiny/interface-details.html", "relUrl": "/interface-details.html" },"16": { "doc": "Interface Details", "title": "General Design Characteristics", - "content": "User Interface and Analysis Features . The cOmicsART user interface evolves gradually to guide users through the necessary steps: . | Data Input Tab: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab. | 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. | 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. Navigation Principles . | 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 | Dropdown Menus: Offer options for selection. Sometime multiple items can be selected. If clicking on a selected item it is removed from the selection | Checkboxes: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated. | 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. | 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 approporiate position. You can use markdown syntax here. | . Features Across Tabs . | 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). | . | Download Options: Users can download autogenerated, HTML reports as well as visualizations and results in common formats (e.g., PNG, XLSX). There are respective buttons. | . ", - "url": "/interface-details.html#general-design-characteristics", + "content": "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. Navigation Principles . | 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 . | 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). | . | 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. | 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. | 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. | 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). | 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. | . ", + "url": "/OmicShiny/interface-details.html#general-design-characteristics", "relUrl": "/interface-details.html#general-design-characteristics" },"17": { "doc": "PCA", "title": "Principle Component Analysis (PCA)", "content": " ", - "url": "/interface-details/pca.html#principle-component-analysis-pca", + "url": "/OmicShiny/interface-details/pca.html#principle-component-analysis-pca", "relUrl": "/interface-details/pca.html#principle-component-analysis-pca" },"18": { "doc": "PCA", "title": "PCA Background", "content": " ", - "url": "/interface-details/pca.html#pca-background", + "url": "/OmicShiny/interface-details/pca.html#pca-background", "relUrl": "/interface-details/pca.html#pca-background" },"19": { "doc": "PCA", "title": "Reactive options", "content": " ", - "url": "/interface-details/pca.html#reactive-options", + "url": "/OmicShiny/interface-details/pca.html#reactive-options", "relUrl": "/interface-details/pca.html#reactive-options" },"20": { "doc": "PCA", "title": "PCA", "content": " ", - "url": "/interface-details/pca.html", + "url": "/OmicShiny/interface-details/pca.html", "relUrl": "/interface-details/pca.html" },"21": { "doc": "Pre-processing", "title": "Pre-processing", "content": " ", - "url": "/interface-details/pre-processing.html", + "url": "/OmicShiny/interface-details/pre-processing.html", "relUrl": "/interface-details/pre-processing.html" },"22": { "doc": "R code", "title": "R code", "content": " ", - "url": "/code-and-data/r-code.html", + "url": "/OmicShiny/code-and-data/r-code.html", "relUrl": "/code-and-data/r-code.html" },"23": { "doc": "Data Input", "title": "The very start", "content": "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 | . | . ", - "url": "/interface-details/required-data-input.html#the-very-start", + "url": "/OmicShiny/interface-details/required-data-input.html#the-very-start", "relUrl": "/interface-details/required-data-input.html#the-very-start" },"24": { "doc": "Data Input", "title": "General remarks on data input", "content": "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. ", - "url": "/interface-details/required-data-input.html#general-remarks-on-data-input", + "url": "/OmicShiny/interface-details/required-data-input.html#general-remarks-on-data-input", "relUrl": "/interface-details/required-data-input.html#general-remarks-on-data-input" },"25": { "doc": "Data Input", "title": "Starting with a single table", "content": "The measurement table . Creating a Sample table . Creating a annotation table . in short . The files must be in the following format: . | 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) | . | 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) | . | 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’. | . ", - "url": "/interface-details/required-data-input.html#starting-with-a-single-table", + "url": "/OmicShiny/interface-details/required-data-input.html#starting-with-a-single-table", "relUrl": "/interface-details/required-data-input.html#starting-with-a-single-table" },"26": { "doc": "Data Input", "title": "Starting with a single table and a Metadatasheet", "content": " ", - "url": "/interface-details/required-data-input.html#starting-with-a-single-table-and-a-metadatasheet", + "url": "/OmicShiny/interface-details/required-data-input.html#starting-with-a-single-table-and-a-metadatasheet", "relUrl": "/interface-details/required-data-input.html#starting-with-a-single-table-and-a-metadatasheet" },"27": { "doc": "Data Input", "title": "Starting with a rds-object", "content": "[advanced] RDS-Structure . ", - "url": "/interface-details/required-data-input.html#starting-with-a-rds-object", + "url": "/OmicShiny/interface-details/required-data-input.html#starting-with-a-rds-object", "relUrl": "/interface-details/required-data-input.html#starting-with-a-rds-object" },"28": { "doc": "Data Input", "title": "Data Input", "content": " ", - "url": "/interface-details/required-data-input.html", + "url": "/OmicShiny/interface-details/required-data-input.html", "relUrl": "/interface-details/required-data-input.html" },"29": { "doc": "Sample correlation", "title": "Sample correlation", "content": " ", - "url": "/interface-details/sample-correlation.html", + "url": "/OmicShiny/interface-details/sample-correlation.html", "relUrl": "/interface-details/sample-correlation.html" },"30": { "doc": "Data Selection", "title": "Data Selection", "content": " ", - "url": "/interface-details/selection.html", + "url": "/OmicShiny/interface-details/selection.html", "relUrl": "/interface-details/selection.html" },"31": { "doc": "Showcase A", "title": "Showcase A", "content": "Details about Showcase A. ", - "url": "/showcases/showcase-a.html", + "url": "/OmicShiny/showcases/showcase-a.html", "relUrl": "/showcases/showcase-a.html" },"32": { "doc": "Showcase A", "title": "Showcase B", "content": "Details about Showcase B. ", - "url": "/showcases/showcase-b.html#showcase-b", + "url": "/OmicShiny/showcases/showcase-b.html#showcase-b", "relUrl": "/showcases/showcase-b.html#showcase-b" },"33": { "doc": "Showcase A", "title": "Showcase A", "content": " ", - "url": "/showcases/showcase-b.html", + "url": "/OmicShiny/showcases/showcase-b.html", "relUrl": "/showcases/showcase-b.html" },"34": { "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": "/showcases.html#showcases-overview", + "url": "/OmicShiny/showcases.html#showcases-overview", "relUrl": "/showcases.html#showcases-overview" },"35": { "doc": "Showcases", "title": "Showcases", "content": " ", - "url": "/showcases.html", + "url": "/OmicShiny/showcases.html", "relUrl": "/showcases.html" },"36": { "doc": "Significance Analysis", "title": "Significance Analysis", "content": " ", - "url": "/interface-details/significance-analysis.html", + "url": "/OmicShiny/interface-details/significance-analysis.html", "relUrl": "/interface-details/significance-analysis.html" },"37": { "doc": "Single Gene Visualisations", "title": "Single Gene Visualisations", "content": " ", - "url": "/interface-details/single-gene-visualisations.html", + "url": "/OmicShiny/interface-details/single-gene-visualisations.html", "relUrl": "/interface-details/single-gene-visualisations.html" },"38": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsArt Documentation 🎨", - "content": ". 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": "/welcome.html#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": { "doc": "Welcome to cOmicsART", "title": "Welcome to cOmicsART", "content": " ", - "url": "/welcome.html", + "url": "/OmicShiny/welcome.html", "relUrl": "/welcome.html" } diff --git a/docs/_site/code-and-data.html b/docs/_site/code-and-data.html index bf11b3c9..c8f3e296 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

Table of contents

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

Table of contents

diff --git a/docs/_site/code-and-data/data.html b/docs/_site/code-and-data/data.html index 8058ebb9..18995560 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
+ Data object | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/code-and-data/examples.html b/docs/_site/code-and-data/examples.html index d9748606..9435addf 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
+ Examples | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/code-and-data/r-code.html b/docs/_site/code-and-data/r-code.html index e42b7a44..a3318bb9 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
+ R code | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/faq.html b/docs/_site/faq.html index 630adf8b..bbb9881d 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

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

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 a760653b..33eb4a23 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

Welcome to cOmicsArt Documentation 🎨

Example Image

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

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 03f4cfb8..343fd71e 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

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

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 e2cae4a7..bb82761c 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

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:

  • Data Input Tab: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab.
  • 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.
  • 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.

  • 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
  • Dropdown Menus: Offer options for selection. Sometime multiple items can be selected. If clicking on a selected item it is removed from the selection
  • Checkboxes: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated.
  • 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.
  • 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 approporiate 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. Download Options: Users can download autogenerated, HTML reports as well as visualizations and results in common formats (e.g., PNG, XLSX). There are respective buttons.
The design of the sidepanel

Table of contents

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

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 025e636a..4caa739e 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
+ Enrichment Analysis | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/interface-details/heatmap.html b/docs/_site/interface-details/heatmap.html index 74285c9c..65059a90 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
+ Heatmap | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/interface-details/pca.html b/docs/_site/interface-details/pca.html index 39c375dc..4eb30339 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

Principle Component Analysis (PCA)

PCA Background

Reactive options

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

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 abd322d3..31981148 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
+ Pre-processing | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/interface-details/required-data-input.html b/docs/_site/interface-details/required-data-input.html index 31b56f1c..5ccf5ff3 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

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

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

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 5d7a7519..4596cde3 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
+ Sample correlation | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/interface-details/selection.html b/docs/_site/interface-details/selection.html index 15249c17..90e1883f 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

Data Selection

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

Data Selection

diff --git a/docs/_site/interface-details/significance-analysis.html b/docs/_site/interface-details/significance-analysis.html index 7978d511..5a3265cf 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
+ Significance Analysis | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/interface-details/single-gene-visualisations.html b/docs/_site/interface-details/single-gene-visualisations.html index 5c6fe4aa..71c43334 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
+ Single Gene Visualisations | cOmicsART Documentation Skip to main content Link Menu Expand (external link) Document Search Copy Copied
diff --git a/docs/_site/showcases.html b/docs/_site/showcases.html index 2546337f..e8e15498 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

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

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 a588f9d0..b93a93a7 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

Showcase A

Details about Showcase A.

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

Showcase A

Details about Showcase A.

diff --git a/docs/_site/showcases/showcase-b.html b/docs/_site/showcases/showcase-b.html index 9f7592c0..61c46268 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

Showcase B

Details about Showcase B.

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

Showcase B

Details about Showcase B.

diff --git a/docs/_site/welcome.html b/docs/_site/welcome.html index cba53561..671367e3 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

Welcome to cOmicsArt Documentation 🎨

Example Image

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

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/index.md b/docs/index.md index ab4cc9b1..614ba5c5 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,10 +7,8 @@ nav_exclude: true # Welcome to cOmicsArt Documentation 🎨 -![Example Image](/OmicShiny/assets/images/cOmicsCat.png) -![Example Image](./OmicShiny/assets/images/cOmicsCat.png) - - +![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsCat.png) +*Image generated using DALL-E by OpenAI. Adjusted by Lea Seep* If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://shiny.iaas.uni-bonn.de/OmicShiny/) diff --git a/docs/interface-details.md b/docs/interface-details.md index d277f54a..22a52610 100644 --- a/docs/interface-details.md +++ b/docs/interface-details.md @@ -15,41 +15,41 @@ If you need tab-specific information, navigate to the respective documentation u The cOmicsART user interface evolves gradually to guide users through the necessary steps: -- **Data Input Tab**: The initial tab where users upload their data. A successful data upload is necessary before accessing the next tab. -- **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. -- **Analysis Tabs**: Six analysis options are available, each in its own tab. These tabs provide interactive result visualizations and various analytical functions. +- 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. - ### Navigation Principles -- **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 -- **Dropdown Menus**: Offer options for selection. Sometime multiple items can be selected. If clicking on a selected item it is removed from the selection -- **Checkboxes**: If a checkbox is clicked, the respective feature is activated. If clicked again, the feature is deactivated. -- **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. -- **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 approporiate position. You can use [markdown syntax](https://www.markdownguide.org/cheat-sheet/) here. - +- 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](https://www.markdownguide.org/cheat-sheet/) 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. -
  2. Download Options: Users can download autogenerated, HTML reports as well as visualizations and results in common formats (e.g., PNG, XLSX). There are respective buttons. -
    3. +
  3. 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).
      • +
    +
    4. +
  4. 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.
    5. +
  5. 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.
    6. +
  6. 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.
    7. +
  7. 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](code-and-data.md).
    8. +
  8. 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 sidepanel +
+
+ The design of the side panel +
- - - diff --git a/docs/welcome.md b/docs/welcome.md index e91ee42f..b84265c8 100644 --- a/docs/welcome.md +++ b/docs/welcome.md @@ -6,7 +6,8 @@ nav_order: 1 # Welcome to cOmicsArt Documentation 🎨 -![Example Image](/OmicShiny/docs/assets/images/cOmicsCat.png) +![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsCat.png) +*Image generated using DALL-E by OpenAI. Adjusted by Lea Seep* If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://comicsart.org/)