plot_ly: Initiate a plotly visualization
In tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

Description Usage Arguments Details Value Author(s) References See Also Examples

This function maps R objects to [plotly.js](https://plot.ly/javascript/), an (MIT licensed) web-based interactive charting library. It provides abstractions for doing common things (e.g. mapping data values to fill colors (via 'color') or creating [animation]s (via 'frame')) and sets some different defaults to make the interface feel more 'R-like' (i.e., closer to [plot()] and [ggplot2::qplot()]).

plot_ly(
  data = data.frame(),
  ...,
  type = NULL,
  name = NULL,
  color = NULL,
  colors = NULL,
  alpha = NULL,
  stroke = NULL,
  strokes = NULL,
  alpha_stroke = 1,
  size = NULL,
  sizes = c(10, 100),
  span = NULL,
  spans = c(1, 20),
  symbol = NULL,
  symbols = NULL,
  linetype = NULL,
  linetypes = NULL,
  split = NULL,
  frame = NULL,
  width = NULL,
  height = NULL,
  source = "A"
)

`data`	A data frame (optional) or [crosstalk::SharedData] object.
`...`	Arguments (i.e., attributes) passed along to the trace 'type'. See [schema()] for a list of acceptable attributes for a given trace 'type' (by going to 'traces' -> 'type' -> 'attributes'). Note that attributes provided at this level may override other arguments (e.g. 'plot_ly(x=1:10, y=1:10, color=I("red"), marker=list(color="blue"))').
`type`	A character string specifying the trace type (e.g. '"scatter"', '"bar"', '"box"', etc). If specified, it always creates a trace, otherwise
`name`	Values mapped to the trace's name attribute. Since a trace can only have one name, this argument acts very much like 'split' in that it creates one trace for every unique value.
`color`	Values mapped to relevant 'fill-color' attribute(s) (e.g. [fillcolor](https://plot.ly/r/reference#scatter-fillcolor), [marker.color](https://plot.ly/r/reference#scatter-marker-color), [textfont.color](https://plot.ly/r/reference/#scatter-textfont-color), etc.). The mapping from data values to color codes may be controlled using 'colors' and 'alpha', or avoided altogether via [I()] (e.g., 'color=I("red")'). Any color understood by [grDevices::col2rgb()] may be used in this way.
`colors`	Either a colorbrewer2.org palette name (e.g. "YlOrRd" or "Blues"), or a vector of colors to interpolate in hexadecimal "#RRGGBB" format, or a color interpolation function like 'colorRamp()'.
`alpha`	A number between 0 and 1 specifying the alpha channel applied to 'color'. Defaults to 0.5 when mapping to [fillcolor](https://plot.ly/r/reference#scatter-fillcolor) and 1 otherwise.
`stroke`	Similar to ‘color', but values are mapped to relevant ’stroke-color' attribute(s) (e.g., [marker.line.color](https://plot.ly/r/reference#scatter-marker-line-color) and [line.color](https://plot.ly/r/reference#scatter-line-color) for filled polygons). If not specified, 'stroke' inherits from 'color'.
`strokes`	Similar to 'colors', but controls the 'stroke' mapping.
`alpha_stroke`	Similar to 'alpha', but applied to 'stroke'.
`size`	(Numeric) values mapped to relevant 'fill-size' attribute(s) (e.g., [marker.size](https://plot.ly/r/reference#scatter-marker-size), [textfont.size](https://plot.ly/r/reference#scatter-textfont-size), and [error_x.width](https://plot.ly/r/reference#scatter-error_x-width)). The mapping from data values to symbols may be controlled using 'sizes', or avoided altogether via [I()] (e.g., 'size=I(30)').
`sizes`	A numeric vector of length 2 used to scale 'size' to pixels.
`span`	(Numeric) values mapped to relevant 'stroke-size' attribute(s) (e.g., [marker.line.width](https://plot.ly/r/reference#scatter-marker-line-width), [line.width](https://plot.ly/r/reference#scatter-line-width) for filled polygons, and [error_x.thickness](https://plot.ly/r/reference#scatter-error_x-thickness)) The mapping from data values to symbols may be controlled using 'spans', or avoided altogether via [I()] (e.g., 'span=I(30)').
`spans`	A numeric vector of length 2 used to scale 'span' to pixels.
`symbol`	(Discrete) values mapped to [marker.symbol](https://plot.ly/r/reference#scatter-marker-symbol). The mapping from data values to symbols may be controlled using 'symbols', or avoided altogether via [I()] (e.g., 'symbol=I("pentagon")'). Any [pch] value or [symbol name](https://plot.ly/r/reference#scatter-marker-symbol) may be used in this way.
`symbols`	A character vector of [pch] values or [symbol names](https://plot.ly/r/reference#scatter-marker-symbol).
`linetype`	(Discrete) values mapped to [line.dash](https://plot.ly/r/reference#scatter-line-dash). The mapping from data values to symbols may be controlled using 'linetypes', or avoided altogether via [I()] (e.g., 'linetype=I("dash")'). Any 'lty' (see [par]) value or [dash name](https://plot.ly/r/reference#scatter-line-dash) may be used in this way.
`linetypes`	A character vector of 'lty' values or [dash names](https://plot.ly/r/reference#scatter-line-dash)
`split`	(Discrete) values used to create multiple traces (one trace per value).
`frame`	(Discrete) values used to create animation frames.
`width`	Width in pixels (optional, defaults to automatic sizing).
`height`	Height in pixels (optional, defaults to automatic sizing).
`source`	a character string of length 1. Match the value of this string with the source argument in [event_data()] to retrieve the event data corresponding to a specific plot (shiny apps can have multiple plots).

Unless 'type' is specified, this function just initiates a plotly object with 'global' attributes that are passed onto downstream uses of [add_trace()] (or similar). A [formula] must always be used when referencing column name(s) in 'data' (e.g. 'plot_ly(mtcars, x=~wt)'). Formulas are optional when supplying values directly, but they do help inform default axis/scale titles (e.g., 'plot_ly(x=mtcars$wt)' vs 'plot_ly(x=~mtcars$wt)')

A plotly

Carson Sievert

<https://plotly-r.com/overview.html>

For initializing a plotly-geo object: [plot_geo()]
For initializing a plotly-mapbox object: [plot_mapbox()]
For translating a ggplot2 object to a plotly object: [ggplotly()]
For modifying any plotly object: [layout()], [add_trace()], [style()]
For linked brushing: [highlight()]
For arranging multiple plots: [subplot()], [crosstalk::bscols()]
For inspecting plotly objects: [plotly_json()]
For quick, accurate, and searchable plotly.js reference: [schema()]

## Not run: 
# plot_ly() tries to create a sensible plot based on the information you
# give it. If you don't provide a trace type, plot_ly() will infer one.
plot_ly(economics, x=~pop)
plot_ly(economics, x=~date, y=~pop)
# plot_ly() doesn't require data frame(s), which allows one to take
# advantage of trace type(s) designed specifically for numeric matrices
plot_ly(z=~volcano)
plot_ly(z=~volcano, type="surface")

# plotly has a functional interface: every plotly function takes a plotly
# object as it's first input argument and returns a modified plotly object
add_lines(plot_ly(economics, x=~date, y=~ unemploy / pop))

# To make code more readable, plotly imports the pipe operator from magrittr
economics %>%
    plot_ly(x=~date, y=~ unemploy / pop) %>%
    add_lines()

# Attributes defined via plot_ly() set 'global' attributes that
# are carried onto subsequent traces, but those may be over-written
plot_ly(economics, x=~date, color=I("black")) %>%
    add_lines(y=~uempmed) %>%
    add_lines(y=~psavert, color=I("red"))

# Attributes are documented in the figure reference -> https://plot.ly/r/reference
# You might notice plot_ly() has named arguments that aren't in this figure
# reference. These arguments make it easier to map abstract data values to
# visual attributes.
p <- plot_ly(iris, x=~Sepal.Width, y=~Sepal.Length)
add_markers(p, color=~Petal.Length, size=~Petal.Length)
add_markers(p, color=~Species)
add_markers(p, color=~Species, colors="Set1")
add_markers(p, symbol=~Species)
add_paths(p, linetype=~Species)

## End(Not run)