Expression

Select marker 1

Contrast marker 1

Select marker 2

``` -------------------------------- ### View Cytomapper Vignette Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/README.md Access the main vignette for the cytomapper package in R to get a comprehensive overview of its analysis workflow and functionality. ```r vignette("cytomapper") ``` -------------------------------- ### Navbar and Download/Help Buttons Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md Illustrates the structure of a Shiny application's navigation bar, including dropdown menus for notifications and tasks. It shows how to implement download links and action buttons for session information and help. ```html ``` -------------------------------- ### Navbar and Download Button Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.new.md Illustrates a navigation bar with a download button and session information/help buttons. The download button is configured for file selection. ```html ``` -------------------------------- ### View plotPixels Function Help Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/README.md Access the detailed help documentation for the plotPixels function in R. This is useful for understanding its parameters and usage. ```r ?plotPixels ``` -------------------------------- ### Sidebar with Range Slider and Sample Selection Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.new.md Demonstrates a sidebar menu with a range slider for plot count and a dropdown for sample selection. Includes navigation buttons for samples. ```html ``` -------------------------------- ### Shiny UI Select Input with Placeholder Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md Illustrates a select input control for choosing an assay, including a placeholder and configuration for maximum items. This is a common pattern for dropdown selections in Shiny. ```html

Select which assay to display

``` -------------------------------- ### View cytomapperShiny Function Help Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/README.md Access the detailed help documentation for the cytomapperShiny function in R. This is useful for understanding its parameters and usage. ```r ?cytomapperShiny ``` -------------------------------- ### Shiny UI with Expression and Contrast Controls Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md This snippet extends the basic layout by adding input fields for contrast markers alongside the expression marker selection. It's used for more detailed analysis where contrast values are needed. ```html

Expression

Select marker 1

Contrast marker 1

Select marker 2

``` -------------------------------- ### View plotCells Function Help Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/README.md Access the detailed help documentation for the plotCells function in R. This is useful for understanding its parameters and usage. ```r ?plotCells ``` -------------------------------- ### Multiple Shiny Sidebar Panels Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.new.md Demonstrates the rendering of multiple sidebar panels with different background colors and distinct input controls. This allows for organizing different sections of a Shiny UI. ```html

Plot 1

Select marker 1

Select marker 2

Plot 2

Select marker 3

Select marker 4

``` -------------------------------- ### Shiny UI Sidebar Rendering Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md Demonstrates the HTML structure for rendering a sidebar in a Shiny application, including placeholder script tags for select inputs. ```html

Plot 3

Select marker 5

Select marker 6

``` -------------------------------- ### Shiny UI Sidebar Navigation Structure Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.new.md Illustrates a common sidebar navigation pattern in Shiny using nested lists for treeview menus. Includes placeholders for dynamic content. ```html ``` -------------------------------- ### Shiny Sidebar with Select Inputs Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md Renders a sidebar panel with two select input dropdowns. Each select input is configured with a placeholder and a maximum of one selectable item. ```html

Plot 1

Select marker 1

Select marker 2

``` -------------------------------- ### Load cytomapper Package in R Session Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/README.md Load the cytomapper package into your current R session to make its functions available for use. ```r library(cytomapper) ``` -------------------------------- ### Shiny UI Select Input with JSON Configuration Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.new.md Renders a select input element within a Shiny UI sidebar. Includes a script tag for JSON configuration, specifying placeholder text and maximum selectable items. ```html

Plot 3

Select marker 5

Select marker 6

``` -------------------------------- ### Multiple Shiny Sidebars with Select Inputs Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md Renders two sidebar panels. The first panel contains two select inputs, and the second panel also contains two select inputs, each with specific styling and JSON configurations. ```html

Plot 1

Select marker 1

Select marker 2

Plot 2

Select marker 3

Select marker 4

``` -------------------------------- ### Citation for Cytomapper Package Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/README.md The recommended citation for the cytomapper R package, including authors, publication details, and DOI. ```text Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller (2020). cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data. Bioinformatics, doi: 10.1093/bioinformatics/btaa1061 ``` -------------------------------- ### Basic Shiny UI Layout with Plots Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md This snippet shows a basic two-column layout in Shiny for displaying expression and selection plots. It includes dropdowns for marker selection and a button to reset markers. ```html

Expression

Select marker 1

Select marker 2

Selection

``` -------------------------------- ### Shiny UI Layout with Expression and Selection Plots Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui_ondisk.md This snippet shows the HTML structure for a Shiny UI layout with two main columns. The left column displays an 'Expression' plot with marker selection controls, and the right column displays a 'Selection' plot. ```html

Expression

Select marker 1

Select marker 2

Selection

``` -------------------------------- ### Shiny Sidebar with Custom Styling Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.new.md Renders a well-styled sidebar panel for a Shiny application. Includes a title and two select input controls with custom JSON configurations. ```html

Plot 1

Select marker 1

Select marker 2

``` -------------------------------- ### Sidebar with General Controls Source: https://github.com/bodenmillergroup/cytomapper/blob/devel/tests/testthat/_snaps/shiny_ui.md Defines a collapsible sidebar menu in a Shiny application, featuring general controls such as a range slider for plot count and navigation for selecting samples. It demonstrates the use of input elements within a structured layout. ```html

General controls