Graph an antibody decay curve model

Description

Graph an antibody decay curve model

Usage

plot_curve_params_one_ab(
  object,
  verbose = FALSE,
  alpha = 0.4,
  n_curves = 100,
  n_points = 1000,
  log_x = FALSE,
  log_y = TRUE,
  iters_to_graph = seq_len(min(n_curves, nrow(object))),
  xlim = c(10^-1, 10^3.1),
  ...
)

Arguments

object a data.frame() of curve parameters (one or more MCMC samples)
verbose verbose output
alpha

(passed to ggplot2::geom_function()) how transparent the curves should be:

  • 0 = fully transparent (invisible)

  • 1 = fully opaque
n_curves how many curves to plot (see details).
n_points Number of points to interpolate along the x axis (passed to ggplot2::geom_function())
log_x should the x-axis be on a logarithmic scale (TRUE) or linear scale (FALSE, default)?
log_y should the Y-axis be on a logarithmic scale (default, TRUE) or linear scale (FALSE)?
iters_to_graph which MCMC iterations in curve_params to plot (overrides n_curves).
xlim range of x values to graph
…

Arguments passed on to ggplot2::geom_function

mapping
Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data
Ignored by stat_function(), do not use.
stat

The statistical transformation to use on the data for this layer. When using a geom_*() function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as “count”.

  • For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as “jitter”.

  • For more information and other ways to specify the position, see the layer position documentation.

arrow
Arrow specification, as created by grid::arrow().
arrow.fill
fill colour to use for the arrow head (if closed). NULL means use colour aesthetic.
lineend
Line end style (round, butt, square).
linejoin
Line join style (round, mitre, bevel).
linemitre
Line mitre limit (number greater than 1).
na.rm
If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend
logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.
inherit.aes
If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn’t inherit behaviour from the default plot specification, e.g. annotation_borders().
geom

The geometric object to use to display the data for this layer. When using a stat_*() function to construct a layer, the geom argument can be used to override the default coupling between stats and geoms. The geom argument accepts the following:

  • A Geom ggproto subclass, for example GeomPoint.

  • A string naming the geom. To give the geom as a string, strip the function name of the geom_ prefix. For example, to use geom_point(), give the geom as “point”.

  • For more information and other ways to specify the geom, see the layer geom documentation.

Details

Fixed … arguments

The arguments fun, n, and args are set internally and cannot be overridden via …. Passing them will trigger an informative error.

n_curves and iters_to_graph

In most cases, object will contain too many rows of MCMC samples for all of these samples to be plotted at once.

  • Setting the n_curves argument to a value smaller than the number of rows in curve_params will cause this function to select the first n_curves rows to graph.

  • Setting n_curves larger than the number of rows in ’ will result all curves being plotted.

  • If the user directly specifies the iters_to_graph argument, then n_curves has no effect.

Value

a ggplot2::ggplot() object

Examples

Code
library("serocalculator")

library(dplyr) # loads the `%>%` operator and `dplyr::filter()`

curve <-
  typhoid_curves_nostrat_100 %>%
  filter(antigen_iso == ("HlyE_IgG")) %>%
  serocalculator:::plot_curve_params_one_ab()

  curve