embed_plotly: Embedding Plot Using the JavaScript Library Plotly

In jlmelville/vizier: Visualization of 2D Datasets in R

Embedding Plot Using the JavaScript Library Plotly

Description

Plots the embedded coordinates, with each point colored by a specified color, using Plotly.

Usage

embed_plotly(
  coords,
  x = NULL,
  colors = NULL,
  color_scheme = NULL,
  num_colors = 15,
  alpha_scale = 1,
  limits = NULL,
  clip_limit_values = TRUE,
  title = NULL,
  show_legend = TRUE,
  cex = 1,
  text = NULL,
  tooltip = NULL,
  equal_axes = FALSE,
  pc_axes = FALSE,
  xlim = NULL,
  ylim = NULL,
  rev = FALSE,
  verbose = FALSE
)

Arguments

coords	Matrix of embedded coordinates, with as many rows as observations, and 2 columns.
x	Either a data frame or a column that can be used to derive a suitable vector of colors. Ignored if colors is provided.
colors	Vector containing colors for each coordinate.
color_scheme	A color scheme. See 'Details'. Ignored if colors is specified.
num_colors	Number of distinct colors to use in the palette, when x is a numeric vector, on the assumption that the palette is continuous (which it probably should be). Ignored if x is not a numeric vector. If set to NULL, it will be set to length(x).
alpha_scale	Scale the opacity alpha of the colors, between 0 and 1. Useful for increasing the transparency of points, especially with large plots with lots of overlap.
limits	The range that the colors should map over when mapping from a numeric vector. If not specified, then the range of x. This is useful if there is some external absolute scale that should be used. Ignored if x is not a numeric vector.
clip_limit_values	If TRUE (the default) and limits is provided, then any value that lies outside the limits is clipped to the limiting values. If tooltip = NULL then the original values will be preserved in the tooltip. If clip_limit_values = FALSE, then values outside the limits will be shown in the "missing" color.
title	Title for the plot.
show_legend	If TRUE, display a legend. Ignored unless a suitable categorical value is provided as x (or one can be found).
cex	Size of the points. Ignored if text is provided.
text	Vector of label text to display instead of a point. If the labels are long or the data set is large, this is unlikely to be very legible, but is occasionally useful.
tooltip	Vector of tooltip text, to be displayed when a point is hovered over.
equal_axes	If TRUE, the X and Y axes are set to have the same extents.
pc_axes	If TRUE, the coords are replaced by the first two (unscaled) principal components, which should have the effect of rotating the data (with a potential reflection) so the main variance aligns along the X-axis. Should not have any other scaling effect.
xlim	Vector two numeric value to give the numeric extent of the X-axis. Ignored if equal_axes = TRUE or pc_axes = TRUE.
ylim	Vector two numeric value to give the numeric extent of the Y-axis. Ignored if equal_axes = TRUE or pc_axes = TRUE.
rev	logical indicating whether the ordering of the colors should be reversed.
verbose	If TRUE, log messages to the console, mainly when searching for a suitable color column in a dataframe. More information on plotly is available at its website, https://plot.ly.

Details

This will open a web browser if you are using the R CLI. In RStudio, it will put the plot in RStudio's Plots tab.

The x argument can be used to provide a suitable vector of colors from either a data frame or vector.

If a data frame is provided, then a vector of colors will be looked for. If it's present, it will be used as the colors argument directly. Otherwise, a factor column will be looked for, and each level will be mapped to a different color. Otherwise, one color will be used for each point. If more than one column of a type is found in the data frame, the last one encountered is used.

If a vector is provided, a similar procedure to the data frame is used when mapping from its content to a vector of colors. Additionally, a numeric vector can be provided, which will be linearly mapped to a color scheme.

The color_scheme parameter can be one of:

• A palette function that takes an integer n and returns a vector of colors, e.g. grDevices::rainbow. For some other applicable functions, see the Palettes help page in the grDevices package (e.g. by running the ?rainbow command).

• A vector of colors making up a custom color scheme of your own devising, e.g. c('red', 'green', 'blue'). There must be at least two colors in the list.

• The name of a color scheme provided by the paletteer package, in the form "package::palette". Some examples include "dutchmasters::milkmaid", "cartography::green.pal", "viridis::inferno" and "RColorBrewer::Dark2". If more colors are required than supported by the color scheme, interpolation will be used to create the required number of colors.

The default for a numeric scale is to use rainbow and for factor columns to use a palette generated by createPalette.

Examples

## Not run: 
# Embed with PCA
pca_iris <- stats::prcomp(iris[, -5], retx = TRUE, rank. = 2)

# Load the plotly package
library("plotly")

# Visualize the resulting embedding, colored by iris species, using the
# rainbow color scheme
embed_plotly(pca_iris$x, iris$Species,
  color_scheme = rainbow,
  title = "iris PCA"
)

# topo.colors scheme
embed_plotly(pca_iris$x, iris$Species, color_scheme = topo.colors)

# Pass in data frame and it will use the last (in this case, only) factor
# column it finds
embed_plotly(pca_iris$x, iris)

# Don't have to see a legend if the tooltips will do
embed_plotly(pca_iris$x, iris, show_legend = FALSE)

# Custom tooltips
embed_plotly(pca_iris$x, iris, tooltip = paste("Species:", iris$Species))

# Use the "Dark2" RColorBrewer scheme
embed_plotly(pca_iris$x, iris, color_scheme = "RColorBrewer::Dark2")

# Can plot the category names instead of points, but looks bad if they're
# long (or the dataset is large)
embed_plot(pca_iris$x, iris$Species, cex = 0.5, text = iris$Species)

# Visualize numeric value (petal length) as a color
embed_plotly(pca_iris$x, iris$Petal.Length, color_scheme = "RColorBrewer::Blues")

# Can force axes to be equal size to stop cluster being distorted in one
# direction
embed_plotly(pca_iris$x, iris$Petal.Length,
  color_scheme = "RColorBrewer::Blues",
  equal_axes = TRUE
)

## End(Not run)

jlmelville/vizier documentation built on Jan. 17, 2024, 8:13 p.m.