R: Plot 'covidcast_signal' object as choropleths, bubbles, or...

plot.covidcast_signal {covidcast}

R Documentation

Plot `covidcast_signal` object as choropleths, bubbles, or time series

Description

Several plot types are provided, including choropleth plots (maps), bubble plots, and time series plots showing the change of signals over time, for a data frame returned by covidcast_signal(). (Only the latest issue from the data frame is used for plotting.) See vignette("plotting-signals", package = "covidcast") for examples.

Usage

## S3 method for class 'covidcast_signal'
plot(
  x,
  plot_type = c("choro", "bubble", "line"),
  time_value = NULL,
  include = c(),
  range = NULL,
  choro_col = c("#FFFFCC", "#FD893C", "#800026"),
  alpha = 0.5,
  bubble_col = "purple",
  num_bins = 8,
  title = NULL,
  choro_params = list(),
  bubble_params = list(),
  line_params = list(),
  ...
)

Arguments

`x`	The `covidcast_signal` object to map or plot. If the object contains multiple issues of the same observation, only the most recent issue is mapped or plotted.
`plot_type`	One of "choro", "bubble", "line" indicating whether to plot a choropleth map, bubble map, or line (time series) graph, respectively. The default is "choro".
`time_value`	Date object (or string in the form "YYYY-MM-DD") specifying the day to map, for choropleth and bubble maps. If `NULL`, the default, then the last date in `x` is used for the maps. Time series plots always include all available time values in `x`.
`include`	Vector of state abbreviations (case insensitive, so "pa" and "PA" both denote Pennsylvania) indicating which states to include in the choropleth and bubble maps. Default is `c()`, which is interpreted to mean all states.
`range`	Vector of two values: min and max, in this order, to use when defining the color scale for choropleth maps and the size scale for bubble maps, or the range of the y-axis for the time series plot. If `NULL`, the default, then for the maps, the min and max are set to be the mean +/- 3 standard deviations, where this mean and standard deviation are as provided in the metadata for the given data source and signal; and for the time series plot, they are set to be the observed min and max of the values over the given time period.
`choro_col`	Vector of colors, as specified in hex code, to use for the choropleth color scale. Can be arbitrary in length. Default is similar to that from https://delphi.cmu.edu/covidcast/.
`alpha`	Number between 0 and 1, indicating the transparency level to be used in the maps. For choropleth maps, this determines the transparency level for the mega counties. For bubble maps, this determines the transparency level for the bubbles. Default is 0.5.
`bubble_col`	Bubble color for the bubble map. Default is "purple".
`num_bins`	Number of bins for determining the bubble sizes for the bubble map (here and throughout, to be precise, by bubble size we mean bubble area). Default is 8. These bins are evenly-spaced in between the min and max as specified through the `range` parameter. Each bin is assigned the same bubble size. Also, values of zero special: it has its own separate (small) bin, and values mapped to the zero bin are not drawn.
`title`	Title for the plot. If `NULL`, the default, then a simple title is used based on the given data source, signal, and time values.
`choro_params`, `bubble_params`, `line_params`	Additional parameter lists for the different plot types, for further customization. See details below.
`...`	Additional arguments, for compatibility with `plot()`. Currently unused.

Details

The following named arguments are supported through the lists choro_params, bubble_params, and line_params.

For both choropleth and bubble maps:

subtitle: Subtitle for the map.
missing_col: Color assigned to missing or NA geo locations.
border_col: Border color for geo locations.
border_size: Border size for geo locations.
legend_position: Position for legend; use "none" to hide legend.
legend_height, legend_width: Height and width of the legend.
breaks: Breaks for a custom (discrete) color or size scale. Note that we must set breaks to be a vector of the same length as choro_col for choropleth maps. This works as follows: we assign the ith color for choropleth maps, or the ith size for bubble maps, if and only if the given value satisfies ⁠breaks[i] <= value < breaks[i+1]⁠, where we take by convention breaks[0] = -Inf and breaks[N+1] = Inf for N = length(breaks).
legend_digits: Number of decimal places to show for the legend labels.

For choropleth maps only:

legend_n: Number of values to label on the legend color bar. Ignored for discrete color scales (when breaks is set manually).

For bubble maps only:

remove_zero: Should zeros be excluded from the size scale (hence effectively drawn as bubbles of zero size)?
min_size, max_size: Min size for the size scale.

For line graphs:

xlab, ylab: Labels for the x-axis and y-axis.
stderr_bands: Should standard error bands be drawn?
stderr_alpha: Transparency level for the standard error bands.

Value

A ggplot object that can be customized and styled using standard ggplot2 functions.