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Plot an Object of Class cs_combined

Source: R/plot.R
plot.cs_combined.Rd

This function creates a generic clinical significance plot by plotting the patients' pre intervention value on the x-axis and the post intervention score on the y-axis.

Usage

# S3 method for cs_combined
plot(
  x,
  x_lab = NULL,
  y_lab = NULL,
  color_lab = "Group",
  lower_limit,
  upper_limit,
  show,
  point_alpha = 1,
  trajectory_alpha = 1,
  rci_fill = "grey10",
  rci_alpha = 0.1,
  overplotting = 0.02,
  ...
)

Arguments

x

An object of class cs_distribution

x_lab

String, x axis label. Default is "Pre".

y_lab

String, x axis label. Default is "Post".

color_lab

String, color label (if colors are displayed). Default is "Group"

lower_limit

Numeric, lower plotting limit. Defaults to 2% smaller than minimum instrument score

upper_limit

Numeric, upper plotting limit. Defaults to 2% larger than maximum instrument score

show

Unquoted category name. You have several options to color different features. Available are

  • category (shows all categories at once)

  • recovered (shows recovered participants)

  • improved (shows improved participants)

  • unchanged (shows unchanged participants)

  • deteriorated (shows deteriorated participants)

  • harmed (shows harmed participants)

point_alpha

Numeric, transparency adjustment for points. A value between 0 and 1 where 1 corresponds to not transparent at all and 0 to fully transparent.

trajectory_alpha

Numeric, transparency adjustment for trajectories. A value between 0 and 1 where 1 corresponds to not transparent at all and 0 to fully transparent.

rci_fill

String, a color (name or HEX code) for RCI fill

rci_alpha

Numeric, controls the transparency of the RCI. This can be any value between 0 and 1, defaults to 0.1

overplotting

Numeric, control amount of overplotting. Defaults to 0.02 (i.e., 2% of range between lower and upper limit).

...

Additional arguments

Value

A ggplot2 plot

Examples

cs_results <- antidepressants |>
  cs_combined(
    patient,
    measurement,
    pre = "Before",
    mom_di,
    reliability = 0.80,
    m_functional = 15,
    sd_functional = 8,
    cutoff_type = "c"
  )


# Plot the results "as is"
plot(cs_results)



# Change the axis labels
plot(cs_results, x_lab = "Before Intervention", y_lab = "After Intervention")



# Show the individual categories
plot(cs_results, show = category)



# Show a specific
plot(cs_results, show = recovered)



# Show groups as specified in the data
cs_results_grouped <- antidepressants |>
  cs_combined(
    patient,
    measurement,
    pre = "Before",
    mom_di,
    reliability = 0.80,
    m_functional = 15,
    sd_functional = 8,
    cutoff_type = "c",
    group = condition
  )

plot(cs_results_grouped)



# To avoid overplotting, generic ggplot2 code can be used to facet the plot
library(ggplot2)
plot(cs_results_grouped) +
  facet_wrap(~ group)



# Adjust the transparency of individual data points
plot(cs_results, point_alpha = 0.3)



# Adjust the fill and transparency of the "unchanged" (RCI) region
plot(cs_results, rci_fill = "firebrick", rci_alpha = 0.2)



# Control the overplotting
plot(cs_results, overplotting = 0.1)



# Or adjust the axis limits by hand
plot(cs_results, lower_limit = 0, upper_limit = 80)