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flextable renders to HTML natively. HTML output uses a scoped <style> block and a Shadow DOM wrapper to isolate table styles from the rest of the page.

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Save to an HTML file

save_as_html() writes one or more flextable objects to a standalone HTML file. Named objects produce <h2> section headings above each table: 
library(flextable)

ft1 <- flextable(head(iris))
tf1 <- tempfile(fileext = ".html")

if (rmarkdown::pandoc_available()) {
  save_as_html(ft1, path = tf1)
}
Multiple tables with section titles: 
ft2 <- flextable(head(mtcars))
tf2 <- tempfile(fileext = ".html")

if (rmarkdown::pandoc_available()) {
  save_as_html(
    `iris table` = ft1,
    `mtcars table` = ft2,
    path = tf2,
    title = "Summary tables"
  )
}
Parameters:
ParameterDescriptionDefault
...flextable objects, optionally named
valuesNamed list of flextable objects (alternative to ...)NULL
pathOutput file path ending in .html
titleHTML page <title>"&#32;"
langIETF language tag for the <html lang> attribute"en"

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Use in Shiny with htmltools_value()

htmltools_value() returns a tagList containing the table HTML and its CSS dependencies. Use it inside renderUI() in Shiny: 
library(shiny)
library(flextable)

ui <- fluidPage(
  uiOutput("ft_table")
)

server <- function(input, output) {
  output$ft_table <- renderUI({
    ft <- flextable(head(iris))
    ft <- autofit(ft)
    htmltools_value(ft)
  })
}

shinyApp(ui, server)
You can control table alignment with the ft.align argument: 
htmltools_value(ft, ft.align = "left")

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Scrollable tables

For large tables, enable scrolling with set_table_properties(): 
ft <- flextable(head(iris, 100))
ft <- set_table_properties(
  ft,
  scroll = list(height = "300px")
)
ft
This wraps the table in a div with overflow-y: auto and a fixed height. You can also freeze the first column: 
ft <- set_table_properties(
  ft,
  scroll = list(
    height = "300px",
    freeze_first_column = TRUE
  )
)
In R Markdown, use the ft.htmlscroll chunk option to enable horizontal scrolling without calling set_table_properties(): 
```{r ft.htmlscroll=TRUE}
flextable(head(iris))
```

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CSS customization

Use set_flextable_defaults(extra_css = ...) to inject additional CSS into every table rendered in the session: 
set_flextable_defaults(
  extra_css = ".tabwid table { font-family: 'Helvetica Neue', sans-serif; }"
)
You can also pass extra CSS directly through set_table_properties(): 
ft <- set_table_properties(
  ft,
  scroll = list(
    height = "400px",
    add_css = "border: 1px solid #ccc;"
  )
)

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HTML dependencies

flextable HTML output depends on a bundled CSS file (tabwid.css). When embedding flextable output in custom htmltools-based pages, retrieve the dependency objects with: 
deps <- flextable_html_dependency()
This returns a list of htmltools::htmlDependency objects that you can attach to your own tags using htmltools::attachDependencies().