InteractiveComplexHeatmap

https://jokergoo.github.io/InteractiveComplexHeatmap/
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InteractiveComplexHeatmap is an R package that converts static heatmaps from ComplexHeatmap into...
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### List Available Examples

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

Execute htShinyExample() with no arguments to get a list of all available examples shipped with the InteractiveComplexHeatmap package. Individual examples can be run by specifying their index.

```r
htShinyExample()
```

--------------------------------

### Example: Get and redraw heatmap positions

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htPositionsOnDevice.html

This example demonstrates how to draw a heatmap, get its positions on the device, and then redraw it using those positions. This is useful for interactive manipulation or precise placement.

```R
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    pos = htPositionsOnDevice(ht)

    InteractiveComplexHeatmap:::redraw_ht_vp(pos)
}
```

--------------------------------

### Interactive heatmap examples

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htShiny.html

Various examples demonstrating how to initialize interactive heatmaps with different configurations and layouts.

```R
# use last generated heatmap
if(interactive() && dev.interactive()) {
    m = matrix(rnorm(100), 10)
    Heatmap(m)
    htShiny()
}

# by providing a heatmap/heatmap list
if(interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    htShiny(ht)
}

# vertical heatmap list
if(interactive()) {
    m1 = matrix(rnorm(100), 10)
    rownames(m1) = 1:10
    colnames(m1) = 1:10
    ht1 = Heatmap(m1, row_km = 2, column_km = 2)

    m2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
    ht2 = Heatmap(m2)

    ht_list = draw(ht1 + ht2)
    htShiny(ht_list)

    ht_list = ht1 %v% ht2
    htShiny(ht_list)
}

# compact mode
if(interactive()) {
    m = matrix(rnorm(100), 10)
    Heatmap(m)
    htShiny(compact = TRUE)
}
```

--------------------------------

### Run InteractiveComplexHeatmap Examples

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/index.html

Use the htShinyExample function to launch built-in interactive examples. Specific examples can be accessed by passing the index as an argument.

```R
htShinyExample()
```

```R
htShinyExample(1.1)
```

```R
htShinyExample('1.10')
```

--------------------------------

### Example Usage (No Example Provided)

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/InteractiveComplexHeatmapOutput.html

The documentation indicates that there are no direct code examples for this function in this section. Refer to the makeInteractiveComplexHeatmap page for usage.

```R
# There is no example
NULL
#> NULL
```

--------------------------------

### Run an Interactive Complex Heatmap Example

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htShinyExample.html

Use htShinyExample to run a specific interactive heatmap example. Call htShinyExample() with no arguments to get a list of available examples.

```R
htShinyExample(which)
```

--------------------------------

### Example of NULL Return

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/getPositionFromHover.html

This example demonstrates the expected output when no hover event has occurred, returning NULL.

```R
NULL
#> NULL
```

--------------------------------

### Launch interactive 2D density visualization

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/interactivate.kde.html

Example usage for creating a kde object and launching the interactive interface.

```R
if(interactive()) {
    require(ks)
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    data = cbind(lt$x, lt$y)
    fit = kde(data)
    interactivate(fit)
}
```

--------------------------------

### Interactive Heatmap Position Selection Example

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/selectPosition.html

This example demonstrates how to create a heatmap and then select a position interactively. Ensure the heatmap is drawn on an interactive graphics device.

```R
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    selectPosition(ht)
}
```

--------------------------------

### Reference sub-heatmap examples

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/subHeatmapOutput.html

Refer to the originalHeatmapOutput help page for usage examples.

```R
# See examples on the help page of originalHeatmapOutput()
```

--------------------------------

### Install Latest Version from GitHub

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/index.html

Install the most recent version of the package directly from GitHub using the devtools package.

```r
library(devtools)
install_github("jokergoo/InteractiveComplexHeatmap")
```

--------------------------------

### Install InteractiveComplexHeatmap from Bioconductor

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/index.html

Use this command to install the package from Bioconductor. Ensure BiocManager is installed first.

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("InteractiveComplexHeatmap")
```

--------------------------------

### Launch Interactive Shiny Heatmap Example

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htShinyExample.html

Executes a specific interactive heatmap example within an active R Shiny session.

```R
if(interactive()) {
    htShinyExample(4.2)
}
```

--------------------------------

### Shiny App Example for Interactive Heatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/InteractiveComplexHeatmapWidget.html

This example demonstrates how to use InteractiveComplexHeatmapWidget within a Shiny application. It sets up a basic UI with a button to trigger heatmap generation and an output area for the heatmap. The server logic creates a heatmap and displays it when the button is clicked.

```R
if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
        htmlOutput("heatmap_output")
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapWidget(input, output, session, ht, 
                output_id = "heatmap_output")
        })
    }
    shiny::shinyApp(ui, server)
}
```

--------------------------------

### Run Specific Interactive Heatmap Example

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

Use `htShinyExample()` to run a specific example by its index. This function makes the interactive heatmap and its source code available on a webpage.

```R
htShinyExample(1.4)
```

--------------------------------

### Shiny App Example for Interactive Heatmap Modal

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/InteractiveComplexHeatmapModal.html

This example demonstrates how to use InteractiveComplexHeatmapModal within a Shiny application. It sets up a basic UI with a button to trigger the heatmap modal and a server function that generates a heatmap and displays it when the button is clicked.

```R
if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapModal(input, output, session, ht)
        })
    }
    shiny::shinyApp(ui, server)
}
```

--------------------------------

### Analyze GO data with GOexpress

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/interactivate_indirect.html

Initial setup and execution of GOexpress analysis to prepare data for heatmap visualization.

```R
library(GOexpress)
data(AlvMac)
set.seed(4543)
AlvMac_results <- GO_analyse(
    eSet = AlvMac, f = "Treatment",
    GO_genes=AlvMac_GOgenes, all_GO=AlvMac_allGO, all_genes=AlvMac_allgenes)
BP.5 <- subset_scores(
    result = AlvMac_results.pVal,
    namespace = "biological_process",
    total = 5,
    p.val=0.05)
heatmap_GO(
    go_id = "GO:0034142", result = BP.5, eSet=AlvMac, cexRow=0.4,
    cexCol=1, cex.main=1, main.Lsplit=30)
```

--------------------------------

### Create a Standalone Shiny App with One Interactive Heatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

This example demonstrates how to create a basic Shiny app that displays a single interactive heatmap. Ensure ComplexHeatmap, InteractiveComplexHeatmap, and shiny libraries are loaded.

```r
library(ComplexHeatmap)
library(InteractiveComplexHeatmap)
library(shiny)

data(rand_mat) # simply a random matrix
ht1 = Heatmap(rand_mat, name = "mat",
    show_row_names = FALSE, show_column_names = FALSE)
ht1 = draw(ht1)

ui = fluidPage(
    h3("My first interactive ComplexHeatmap Shiny app"),
    p("This is an interactive heatmap visualization on a random matrix."),
    InteractiveComplexHeatmapOutput()
)

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht1)
}

shinyApp(ui, server)
```

--------------------------------

### Interactive heatmap area selection examples

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/selectArea.html

Demonstrates how to use selectArea in an interactive R session with standard and k-means clustered heatmaps.

```R
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    selectArea(ht)

    set.seed(123)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    selectArea(ht)
}
```

--------------------------------

### Customizing Heatmap Output with Shiny

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

This example demonstrates how to replace the default UI with a custom htmlOutput and define server-side click and brush actions to display styled text and tables of selected heatmap data. Requires the GetoptLong, kableExtra, and InteractiveComplexHeatmap packages.

```R
library(GetoptLong)  # for the qq() function which does variable intepolation
data(rand_mat)
ht = Heatmap(rand_mat, show_row_names = FALSE, show_column_names = FALSE)
ht = draw(ht)

ui = fluidPage(
    InteractiveComplexHeatmapOutput(output_ui = htmlOutput("info")),
)

click_action = function(df, output) {
    output[["info"]] = renderUI({
        if(!is.null(df)) {
            HTML(qq("<p style='background-color:#FF8080;color:white;padding:5px;'>You have clicked on heatmap @{df$heatmap}, row @{df$row_index}, column @{df$column_index}</p>"))
        }
    })
}

suppressPackageStartupMessages(library(kableExtra))
brush_action = function(df, output) {
    row_index = unique(unlist(df$row_index))
    column_index = unique(unlist(df$column_index))
    output[["info"]] = renderUI({
        if(!is.null(df)) {
            HTML(kable_styling(kbl(m[row_index, column_index, drop = FALSE], digits = 2, format = "html"), full_width = FALSE, position = "left"))
        }
    })
}

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht,
        click_action = click_action, brush_action = brush_action)
}

shinyApp(ui, server)
```

--------------------------------

### Implement interactive heatmap in a Shiny application

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/makeInteractiveComplexHeatmap.html

A complete example demonstrating the integration of a heatmap into a Shiny UI and server function.

```R
if(interactive()) {
    ht = Heatmap(m)
    ht = draw(ht)

    ui = fluidPage(
        InteractiveComplexHeatmapOutput()
    )

    server = function(input, output, session) {
        makeInteractiveComplexHeatmap(input, output, session, ht)
    }

    shiny::shinyApp(ui, server)
}
```

--------------------------------

### Implement Interactive Complex Heatmap in Shiny

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/originalHeatmapOutput.html

Demonstrates a full Shiny application setup using originalHeatmapOutput, subHeatmapOutput, and HeatmapInfoOutput within a dashboard layout.

```R
if(interactive()) {
    require(shinydashboard)
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m)

    body = dashboardBody(
        fluidRow(
            box(title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
                originalHeatmapOutput("ht")
            ),
            box(title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
                subHeatmapOutput("ht")
            ),
            box(title = "Output", width = 4, solidHeader = TRUE, status = "primary",
                HeatmapInfoOutput("ht")
            )
        )
    )
    ui = dashboardPage(
        dashboardHeader(),
        dashboardSidebar(),
        body
    )
    server = function(input, output, session) {
        makeInteractiveComplexHeatmap(input, output, session, ht, "ht")
    }
    shinyApp(ui, server)
}
```

--------------------------------

### Creating Interactive Shiny Apps with DESeq2 Data

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/deseq2_app.html

This example demonstrates how to use the `interactivate()` function to generate a Shiny app directly from a DESeqDataSet object. Ensure DESeq2 and airway packages are loaded.

```R
library(DESeq2)
library(airway)
data(airway)

dds = DESeqDataSet(airway, design = ~ dex)
dds = DESeq(dds)

interactivate(dds)
```

--------------------------------

### Implement custom heatmap interactivity in Shiny

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

A complete Shiny application example that captures click and brush events on a heatmap to output the selected data.

```R
ui = fluidPage(
    actionButton("action", "Generate heatmap"),
    plotOutput("heatmap", width = 500, height = 500, click = "heatmap_click", 
        brush = "heatmap_brush"),
    verbatimTextOutput("output")
)
server = function(input, output, session) {

    ht_obj = reactiveVal(NULL)
    ht_pos_obj = reactiveVal(NULL)

    observeEvent(input$action, {
        m = matrix(rnorm(100), 10)
        rownames(m) = 1:10
        colnames(m) = 1:10

        output$heatmap = renderPlot({
            ht = draw(Heatmap(m))
            ht_pos = htPositionsOnDevice(ht)

            ht_obj(ht)
            ht_pos_obj(ht_pos)
        })
    })

    observeEvent(input$heatmap_click, {
        pos = getPositionFromClick(input$heatmap_click)

        selection = selectPosition(ht_obj(), pos, mark = FALSE, ht_pos = ht_pos_obj(), 
            verbose = FALSE)
        output$output = renderPrint({
            print(selection)
        })
    })

    observeEvent(input$heatmap_brush, {
        lt = getPositionFromBrush(input$heatmap_brush)

        selection = selectArea(ht_obj(), lt[[1]], lt[[2]], mark = FALSE, ht_pos = ht_pos_obj(), 
            verbose = FALSE)
        output$output = renderPrint({
            print(selection)
        })
    })
}
shinyApp(ui, server)
```

--------------------------------

### Example Usage of interactivateDensity2D

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/interactivateDensity2D.html

This example demonstrates how to use the interactivateDensity2D function within an interactive Shiny session. It first reads RDS data and then calls the function with the extracted x and y components.

```R
if(interactive()) {
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    interactivateDensity2D(lt$x, lt$y)
}
```

--------------------------------

### Arrange Multiple Interactive Heatmaps Using Tabsets

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

This example demonstrates arranging multiple interactive heatmaps within a Shiny app using tabsets. Each heatmap is placed in a separate tab and requires a unique 'heatmap ID'.

```r
ui = tabsetPanel(
    tabPanel("Numeric", InteractiveComplexHeatmapOutput("heatmap_1")),
    tabPanel("character", InteractiveComplexHeatmapOutput("heatmap_2"))
)
server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht1, "heatmap_1")
    makeInteractiveComplexHeatmap(input, output, session, ht2, "heatmap_2")
}
shinyApp(ui, server)
```

--------------------------------

### InteractiveComplexHeatmapModal Function

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/InteractiveComplexHeatmapModal.html

This snippet details the InteractiveComplexHeatmapModal function, its arguments, and provides a full example of its implementation in a Shiny application.

```APIDOC
## InteractiveComplexHeatmapModal Function

### Description
It creates an interactive heatmap "modal dialog" according to a certain action. The function is normally put inside `observe` or `observeEvent`.

### Method
`InteractiveComplexHeatmapModal()`

### Endpoint
N/A (This is a function within a Shiny application)

### Parameters
#### Arguments
- **input** (Shiny input object) - Passed from the Shiny server function.
- **output** (Shiny output object) - Passed from the Shiny server function.
- **session** (Shiny session object) - Passed from the Shiny server function.
- **ht_list** (Heatmap-class or HeatmapList-class object) - A `Heatmap-class` or a `HeatmapList-class` object.
- **heatmap_id** (character, optional) - ID of the plot. If it is not specified, an internal ID is assigned.
- **title1** (character) - Pass to `InteractiveComplexHeatmapOutput`. Default: "Original heatmap".
- **title2** (character) - Pass to `InteractiveComplexHeatmapOutput`. Default: "Selected sub-heatmap".
- **width1** (numeric) - Pass to `InteractiveComplexHeatmapOutput`. Default: `ifelse(layout == "1|(2-3)", 800, 450)`.
- **height1** (numeric) - Pass to `InteractiveComplexHeatmapOutput`. Default: `ifelse(layout == "1-(2|3)", 700, 350)`.
- **width2** (numeric) - Pass to `InteractiveComplexHeatmapOutput`. Default: 370.
- **height2** (numeric) - Pass to `InteractiveComplexHeatmapOutput`. Default: 350.
- **width3** (numeric) - Pass to `InteractiveComplexHeatmapOutput`. Default: `ifelse(layout == "(1-2)|3", 800, 370)`.
- **layout** (character) - Pass to `InteractiveComplexHeatmapOutput`. Default: `ifelse("brush" %in% response, "(1-2)|3", "1-3")`.
- **compact** (logical) - Pass to `InteractiveComplexHeatmapOutput`. Default: FALSE.
- **action** (character) - Pass to `InteractiveComplexHeatmapOutput`. Default: "click".
- **cursor** (logical) - Pass to `InteractiveComplexHeatmapOutput`. Default: TRUE.
- **response** (character vector) - Pass to `InteractiveComplexHeatmapOutput`. Default: `c(action, "brush")`.
- **brush_opt** (list) - Pass to `InteractiveComplexHeatmapOutput`. Default: `list(stroke = "#f00", opacity = 0.6)`.
- **output_ui** (logical) - Pass to `InteractiveComplexHeatmapOutput`. Default: TRUE.
- **output_ui_float** (logical) - Pass to `InteractiveComplexHeatmapOutput`. Default: FALSE.
- **click_action** (function, optional) - Pass to `makeInteractiveComplexHeatmap`.
- **brush_action** (function, optional) - Pass to `makeInteractiveComplexHeatmap`.
- **js_code** (character or function) - Additional JavaScript code that is put after the interactive heatmap UI. The value can be a text or a function that takes "heatmap ID" as the argument and returns the formatted JavaScript code.
- **close_button** (logical) - Whether to add a close button at the end of the widget. Default: TRUE.
- **cancel_action** (character vector) - Whether to remove the UI from HTML or just hide it when the UI is closed. Default: `c("remove", "hide")`.

### Value
No value is returned.

### Examples
```r
if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapModal(input, output, session, ht)
        })
    }
    shiny::shinyApp(ui, server)
}
```
```

--------------------------------

### Integrate Multiple Interactive Heatmaps in a Single Shiny App

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

This example shows how to embed multiple interactive heatmaps in one Shiny app. Each heatmap must be assigned a unique 'heatmap ID' starting with a letter.

```r
mat2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
ht2 = draw(Heatmap(mat2, name = "mat2"))

ui = fluidPage(
    h3("The first heatmap"),
    InteractiveComplexHeatmapOutput("heatmap_1"),
    hr(),
    h3("The second heatmap"),
    InteractiveComplexHeatmapOutput("heatmap_2")
)
server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht1, "heatmap_1")
    makeInteractiveComplexHeatmap(input, output, session, ht2, "heatmap_2")
}
shinyApp(ui, server)
```

--------------------------------

### Viewing the Launch Output

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/share.html

Executing the launch script provides a local URL to access the interactive heatmap in a web browser.

```bash
guz@B069-mb04:~/test_ht$ sh htShiny.sh
If the shiny app is not automatically opened in the browser, you can manually
copy the following link and paste it to the browser.
Listening on http://127.0.0.1:4132
```

--------------------------------

### Launching a Shiny Application

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/deseq2_app.html

This code snippet shows how to launch a Shiny application using the ui and server components.

```R
shinyApp(ui, server)
```

--------------------------------

### Get Click Position from Heatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/getPositionFromClick.html

Use this function to get the coordinates of a click on the heatmap. Ensure the click object is correctly set up in plotOutput.

```R
getPositionFromClick(click, ratio = 1)
```

```R
NULL
```

--------------------------------

### Get Hover Position from Heatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/getPositionFromHover.html

Use this function to get the coordinates of a hovered point on the heatmap image. The `hover` argument should be the ID set in `plotOutput`, and `ratio` is the relative resolution.

```R
getPositionFromHover(hover, ratio = 1)
```

--------------------------------

### Interactive visualization of DESeq2 results

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/interactivate.DESeqDataSet.html

Demonstrates how to prepare a DESeqDataSet and launch the interactive visualization.

```R
if(interactive()) {
    require(airway)
    data(airway)
    se = airway

    require(DESeq2)
    dds = DESeqDataSet(se, design = ~ dex)
    keep = rowSums(counts(dds)) >= 10
    dds = dds[keep, ]
    dds$dex = relevel(dds$dex, ref = "untrt")
    dds = DESeq(dds)

    interactivate(dds)
}
```

--------------------------------

### Get Position From Click

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/getPositionFromClick.html

Retrieves the coordinates of a clicked point on the heatmap image.

```APIDOC
## GET /getPositionFromClick

### Description
Get the position of clicked point on the heatmap image.

### Method
GET

### Endpoint
/getPositionFromClick

### Parameters
#### Query Parameters
- **click** (object) - Required - The input click object. Assume `heatmap_click` is the ID set to argument `click` in `plotOutput`, then the value here is `input$heatmap_click`.
- **ratio** (numeric) - Optional - The relative resolution. The value should be the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`).

### Response
#### Success Response (200)
- **unit** (object) - A `unit` object of length two which are the coordinates of the clicked points.

### See Also
`getPositionFromBrush`, `getPositionFromHover`, `getPositionFromDblclick`
```

--------------------------------

### Get Position from Double Click

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/getPositionFromDblclick.html

Retrieves the coordinates of a double-clicked point on the heatmap image.

```APIDOC
## GET /getPositionFromDblclick

### Description
Get the position of double clicked point on the heatmap image.

### Method
GET

### Endpoint
/getPositionFromDblclick

### Parameters
#### Query Parameters
- **dblclick** (object) - Required - The input dblclick object. Assume `heatmap_dblclick` is the ID set to argument `dblclick` in `plotOutput`, then the value here is `input$heatmap_dblclick`.
- **ratio** (numeric) - Optional - The relative resolution. The value should be the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`).

### Response
#### Success Response (200)
- **coordinates** (unit object) - A `unit` object of length two which are the coordinates of the double clicked points.

### Response Example
```json
{
  "coordinates": ["100px", "50px"]
}
```
```

--------------------------------

### Get all row indices from a data frame

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/all_row_indices.html

This function retrieves all row indices from the selected data frame.

```APIDOC
## GET /websites/jokergoo_github_io_interactivecomplexheatmap/all_row_indices

### Description
Retrieves all row indices from the selected data frame.

### Method
GET

### Endpoint
/websites/jokergoo_github_io_interactivecomplexheatmap/all_row_indices

### Parameters
#### Query Parameters
- **df** (data.frame) - Required - The selected data frame.

### Response
#### Success Response (200)
- **indices** (integer array) - A list of all row indices from the data frame.

#### Response Example
```json
{
  "indices": [1, 2, 3, 4, 5]
}
```
```

--------------------------------

### interactivate

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/interactivate.kde.html

Launches an interactive Shiny application for visualizing a 2D density distribution based on a kde object.

```APIDOC
## interactivate

### Description
Launches an interactive Shiny application for visualizing a 2D density distribution based on a kde object.

### Method
S3 method

### Endpoint
interactivate(x, ...)

### Parameters
#### Arguments 
- **x** (kde object) - A `kde` object generated by `kde`.
- **...** (Other arguments) - Other arguments that can be passed to the function.

### Request Example
__```R
if(interactive()) {
    require(ks)
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    data = cbind(lt$x, lt$y)
    fit = kde(data)
    interactivate(fit)
}
```
```

--------------------------------

### Get all column indices from the selected data frame

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/all_column_indices.html

This function retrieves all column indices from a given data frame.

```APIDOC
## GET /all_column_indices

### Description
Retrieves all column indices from the selected data frame.

### Method
GET

### Endpoint
/all_column_indices

### Parameters
#### Query Parameters
- **df** (data.frame) - Required - The selected data frame.

### Request Example
```json
{
  "df": "your_data_frame_here"
}
```

### Response
#### Success Response (200)
- **indices** (list) - A list of column indices.

#### Response Example
```json
{
  "indices": [1, 2, 3, 4, 5]
}
```
```

--------------------------------

### Deploying to Shiny Server

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/share.html

Use the rsconnect package to deploy the application to a Shiny Server environment.

```R
rsconnect::setAccountInfo(...)
rsconnect::deployApp(...)
```

--------------------------------

### Basic Shiny App with Interactive Heatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/index.html

Create a simple Shiny app with an interactive heatmap. Requires `InteractiveComplexHeatmap` and `ComplexHeatmap` libraries. `InteractiveComplexHeatmapOutput` is used in the UI and `makeInteractiveComplexHeatmap` in the server.

```r
library(InteractiveComplexHeatmap)
library(ComplexHeatmap)

ht = Heatmap(m)
ht = draw(ht)

ui = fluidPage(
    InteractiveComplexHeatmapOutput()
)

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht)
}

shiny::shinyApp(ui, server)
```

--------------------------------

### Define interactivate method for kde

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/interactivate.kde.html

Signature for the S3 method used to launch the interactive Shiny application.

```R
# S3 method for kde
interactivate(x, ...)
```

--------------------------------

### Launching the Interactive Heatmap Locally

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/share.html

Collaborators can launch the heatmap using the provided shell or batch scripts, or by running the R script directly.

```bash
cd ~/test_ht
sh htShiny.sh
# or
Rscript htShiny.R
```

--------------------------------

### Get Position From Brush

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/getPositionFromBrush.html

Retrieves the coordinates of the brushed area on the heatmap image. This function is typically used in conjunction with Shiny applications where brush events are captured.

```APIDOC
## GET /getPositionFromBrush

### Description
Get the position of the brushed area on the heatmap image.

### Method
GET

### Endpoint
/getPositionFromBrush

### Parameters
#### Query Parameters
- **brush** (object) - Required - The input brush object. Assume `heatmap_brush` is the ID set to argument `brush` in `plotOutput`, then the value here is `input$heatmap_brush`.
- **ratio** (numeric) - Optional - The relative resolution. The value should be the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`). Defaults to 1.

### Response
#### Success Response (200)
- **list** (list) - A list of length two. The two elements correspond to the coordinates of the two diagonal points.

#### Response Example
```json
{
  "coordinates": [
    {"x": 10, "y": 20},
    {"x": 50, "y": 60}
  ]
}
```
```

--------------------------------

### Generate Interactive Heatmap with tidyHeatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

This code demonstrates how to create a tidy heatmap from the mtcars dataset and export it as an interactive Shiny app. Ensure tidyverse and tidyheatmap are installed.

```r
library(tidyverse)
library(tidyHeatmap)
mtcars_tidy <- 
    mtcars %>% 
    as_tibble(rownames="Car name") %>% 
    mutate_at(vars(-`Car name`, -hp, -vs), scale) %>%
    pivot_longer(cols = -c(`Car name`, hp, vs), names_to = "Property", values_to = "Value")

mtcars_heatmap <- 
    mtcars_tidy %>% 
        heatmap(`Car name`, Property, Value ) %>%
        add_tile(hp)

htShiny(mtcars_heatmap)
```

--------------------------------

### Get heatmap positions on the graphics device

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htPositionsOnDevice.html

Retrieves the positions of heatmap components on the active graphics device. This function is useful for precise layout control and further manipulation of heatmap elements.

```APIDOC
## htPositionsOnDevice

### Description
Get heatmap positions on the graphics device.

### Method
`htPositionsOnDevice`

### Endpoint
N/A (R function)

### Parameters
#### Arguments 
- **ht_list** (HeatmapList-class) - Optional - A `HeatmapList-class` object returned by `draw,Heatmap-method` or `draw,HeatmapList-method`. If it is omitted, it uses the last generated heatmap.
- **unit** (string) - Optional - The unit for positioning (e.g., "inch", "cm", "mm", "pt", "native").
- **valueOnly** (boolean) - Optional - Whether only return the numeric values of the positions.
- **include_annotation** (boolean) - Optional - Internally used parameter.
- **calibrate** (boolean) - Optional - Internally used parameter.

### Details
`ht_list` must have been already updated by `draw()` function. The function needs to be executed under a graphics device where the heatmap is written.

### Value
It returns a `DataFrame` object of the position of every heatmap slice.

### Request Example
```R
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    pos = htPositionsOnDevice(ht)

    InteractiveComplexHeatmap:::redraw_ht_vp(pos)
}
```

### Response Example
(DataFrame object with position information)
```

--------------------------------

### Get heatmap positions on device

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htPositionsOnDevice.html

Retrieves the positions of heatmap slices on the graphics device. Ensure the heatmap has been drawn to the device before calling this function. It returns a DataFrame of slice positions.

```R
htPositionsOnDevice(ht_list = get_last_ht(), unit = "inch", valueOnly = FALSE, include_annotation = FALSE, calibrate = TRUE)
```

--------------------------------

### Generate Dynamic Heatmap in Modal based on Selection

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Demonstrates generating different heatmaps based on user radio button selection within a modal.

```R
ui = fluidPage(
    radioButtons("select", "Select", c("Numeric" = 1, "Character" = 2)),
    actionButton("show_heatmap", "Generate_heatmap"),
)

get_heatmap_fun = function(i) {
    mat_list = list(
        matrix(rnorm(100), 10),
        matrix(sample(letters[1:10], 100, replace = TRUE), 10)
    )
    Heatmap(mat_list[[i]])
}

server = function(input, output, session) {
    observeEvent(input$show_heatmap, {
        i = as.numeric(input$select)
        InteractiveComplexHeatmapModal(input, output, session, 
            get_heatmap = get_heatmap_fun(i))
    })
}
shiny::shinyApp(ui, server)
```

--------------------------------

### Simulating Position Selection in PDF Device

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/implementation.html

Simulates a single click position on a heatmap within a PDF graphics device by providing `pos` argument to `selectPosition()`. The output DataFrame contains the selected point's coordinates and corresponding heatmap data.

```R
pdf(...)
ht_list = draw(ht_list)
pos = selectPosition(ht_list, pos = unit(c(3, 3), "cm"))
dev.off()
```

```R
pos
```

--------------------------------

### Create Interactive Enriched Heatmap (Combined)

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

Exports a combined enriched heatmap with additional heatmaps as a Shiny app. Requires matrices to be normalized.

```r
ht = EnrichedHeatmap(mat, ...) + EnrichedHeatmap(...) + Heatmap(...)
htShiny(ht)
```

--------------------------------

### Define UI with Custom Output for Heatmap Actions

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Use `InteractiveComplexHeatmapOutput` with `output_ui` to specify where heatmap interaction outputs should be displayed. This integrates the output directly within the heatmap widget.

```R
ui = fluidPage(
    InteractiveComplexHeatmapOutput(output_ui = htmlOutput("info"))
)
```

--------------------------------

### Basic usage of htShiny

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htShiny.html

Directly pass a heatmap object or use the last generated heatmap to create an app.

```R
    htShiny(ht_list)
```

```R
    Heatmap(...) + other_heatmaps_or_annotations # or other functions that internally use Heatmap()
    htShiny()
```

--------------------------------

### Implement custom heatmap interaction in Shiny

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/from_scratch.html

Demonstrates the use of low-level functions to capture click events and retrieve selected heatmap cell information.

```R
ui = fluidPage(
    ...,
    plotOutput("heatmap", click = "heatmap_click")
)
server = function(input, output, session) {
    ht_obj = reactiveVal(NULL)
    ht_pos_obj = reactiveVal(NULL)
    output$heatmap = renderPlot({
        ...
        ht = draw(Heatmap(mat))
        ht_pos = htPositionsOnDevice(ht)
        ht_obj(ht)
        ht_pos_obj(ht_pos)
    })
    observeEvent(input$heatmap_click, {
        pos = getPositionFromClick(input$heatmap_click)
        df = selectPosition(ht_obj(), pos, mark = FALSE, 
            ht_pos = ht_pos_obj(), verbose = FALSE)
        # do something with `df`
        ...
    })
}
```

--------------------------------

### Integrate with shinydashboard

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Use individual output functions to place heatmap components into separate dashboard boxes.

```R
body = dashboardBody(
    fluidRow(
        box(
            title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
            originalHeatmapOutput("ht", title = NULL)
        ),
        box(
            title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
            subHeatmapOutput("ht", title = NULL)
        ),
        box(
            title = "Output", width = 4, solidHeader = TRUE, status = "primary",
            HeatmapInfoOutput("ht", title = NULL)
        )
    )
)

ui = dashboardPage(
    dashboardHeader(),
    dashboardSidebar(),
    body
)

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht, "ht")
}

shinyApp(ui, server)
```

--------------------------------

### Basic Structure for Custom Click/Brush Action Function

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Define a function to handle heatmap interactions. This function receives a DataFrame `df` with selected information and an `output` object to render UI elements. It should include checks for `NULL` df to handle cases where no heatmap body was selected.

```R
function(df, output) {
    output[["info"]] = renderUI({  # or output$info = ...
        if(is.null(df)) { # have not clicked or brushed into the heatmap body
            ...
        } else {
            ...
        }
    })
}
```

--------------------------------

### htShinyExample Function

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/htShinyExample.html

Launches a Shiny application demonstrating interactive complex heatmaps based on the provided index.

```APIDOC
## htShinyExample

### Description
Launches a Shiny app that demonstrates interactive complex heatmaps. Each example includes the source code used to generate the application.

### Parameters
#### Arguments
- **which** (index) - Optional - An index of which example to use. If no argument is provided, the function returns a list of all available examples.

### Value
- **Shiny app object** - Returns a Shiny application object.
```

--------------------------------

### Display Session Information

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

The `sessionInfo()` function displays details about the R session, including version, platform, and loaded packages. This is useful for debugging and reproducibility.

```R
sessionInfo()
```

--------------------------------

### Create Interactive Enriched Heatmap (Single)

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

Exports a single enriched heatmap generated by EnrichedHeatmap() as a Shiny app. Requires a matrix 'mat' to be normalized.

```r
mat = normalizeToMatrix(...)
ht = EnrichedHeatmap(mat, ...)
htShiny(ht)
```

--------------------------------

### Exporting Interactive Heatmap to a Local Folder

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/share.html

Use the save argument in htShiny to generate a directory containing the necessary R scripts and data for offline execution.

```R
# E.g. the folder is "test_ht"
htShiny(ht, save = "test_ht")
```

--------------------------------

### Create Interactive OncoPrint (Combined)

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

Exports a combined oncoPrint with additional heatmaps and annotations as a Shiny app. Ensure oncoPrint and Heatmap/rowAnnotation are called with appropriate arguments.

```r
ht = oncoPrint(...) + Heatmap(...) + rowAnnotation(...)
htShiny(ht)
```

--------------------------------

### Generate Heatmap List

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/implementation.html

Create a list of two heatmaps with k-means clustering applied to the first matrix.

```R
library(ComplexHeatmap)
library(InteractiveComplexHeatmap)
set.seed(123)
mat1 = matrix(rnorm(100), 10)
rownames(mat1) = colnames(mat1) = paste0("a", 1:10)
mat2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
rownames(mat2) = colnames(mat2) = paste0("b", 1:10)

ht_list = Heatmap(mat1, name = "mat_a", row_km = 2, column_km = 2) +
    Heatmap(mat2, name = "mat_b")
```

--------------------------------

### Create Interactive Density Heatmap

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/InteractiveComplexHeatmap_intro.html

Exports a density heatmap generated by ComplexHeatmap::densityHeatmap() as a Shiny app. Ensure densityHeatmap is called with appropriate arguments.

```r
ht = densityHeatmap(...)
htShiny(ht)
```

--------------------------------

### Define UI with Independent Custom Output for Heatmap Actions

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Alternatively, create a separate `htmlOutput` element in the UI to display heatmap interaction results independently of the heatmap widget itself.

```R
ui = fluidPage(
    InteractiveComplexHeatmapOutput(),
    htmlOutput("info")
)
```

--------------------------------

### Add CSS for shinydashboard layout

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Include custom CSS to ensure proper overflow and minimum width when using dashboard boxes.

```R
body = dashboardBody(
    fluidRow(
        box(
            title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
            originalHeatmapOutput("ht", title = NULL)
        ),
        box(
            title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
            subHeatmapOutput("ht", title = NULL)
        ),
        box(
            title = "Output", width = 4, solidHeader = TRUE, status = "primary",
            HeatmapInfoOutput("ht", title = NULL)
        ),
        tags$style("
            .content-wrapper, .right-side {
                overflow-x: auto;
            }
            .content {
                min-width:1500px;
            }
        ")
    )
)
```

--------------------------------

### Compact Mode for Interactive Heatmaps

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/shiny_dev.html

Enables compact mode for InteractiveComplexHeatmap, where the output floats to the mouse position upon hovering or clicking. This is equivalent to setting output_ui_float = TRUE and response to include 'brush-output'.

```R
InteractiveComplexHeatmapOutput(..., compact = TRUE)
```

```R
InteractiveComplexHeatmap(..., compact = TRUE, output_ui = new_output_ui)
```

--------------------------------

### Generate the rand_mat dataset

Source: https://jokergoo.github.io/InteractiveComplexHeatmap/reference/rand_mat.html

Constructs the 60x60 random matrix using normal distributions with specific means and standard deviations.

```R
  set.seed(123)
  rand_mat = cbind(rbind(matrix(rnorm(20*20, mean = 1, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20)),
            rbind(matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 1, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20)),
            rbind(matrix(rnorm(20*20, mean = 0.5, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0.5, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 1, sd = 0.5), nr = 20))
           ) + matrix(rnorm(60*60, sd = 0.5), nr = 60)
   colnames(rand_mat) = paste0("C", 1:60)
   rownames(rand_mat) = paste0("R", 1:60)
```
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