toxFigures {ProAE} | R Documentation |
Create PRO-CTCAE severity frequency distribution figures for individual survey items and composite scores
Description
Data format should be in 'long' format, where each PRO-CTCAE item is a variable/column.
Usage
toxFigures(
dsn,
id_var,
cycle_var,
baseline_val,
arm_var = NA,
plot_limit = NA,
colors = 1,
bar_label = 0,
cycle_label = FALSE,
cycle_vals = NA,
cycle_labs = NA,
summary_only = FALSE,
summary_highlight = FALSE,
cycles_only = TRUE,
x_lab_angle = 0,
x_lab_vjust = 1,
x_lab_hjust = 0,
x_label = "Randomized Treatment Assignment",
y_label = "Percent of Total Frequency",
footnote_break = FALSE,
suppress_legend = FALSE,
add_item_title = FALSE
)
Arguments
dsn |
A data.frame object with PRO-CTCAE data |
id_var |
A character string.Name of ID variable differentiating each PRO-CTCAE survey/participant entered as a quoted string. |
cycle_var |
A character string. Name of variable differentiating one longitudinal/repeated PRO-CTCAE survey from another, within an individual ID. |
baseline_val |
A number indicating the expected baseline cycle/time point. |
arm_var |
A character string. Name of arm variable differentiating
treatment groups. Must be character or factor class. Overall AUC
will be reported if no arm/grouping variable is provided. Defaults to
|
plot_limit |
A number. Limit the number of cycles to be plotted up to
and including a given cycle number. All available cycle time points are
plotted if no cycle number is provided. Defaults to |
colors |
A number. Specify the coloring scheme of symptom scores within frequency bars. Options include: 1 = Blue and red color shading, 2 = qualitative color shades (color blind friendly), 3 = black and white. Defaults to 1. |
bar_label |
A number. Label frequency bars with sample size (n) or percent
shown on the y-axis. Label options include: |
cycle_label |
Logical. Assign custom labels to cycles/time point. If
|
cycle_vals |
Numeric column vector. Vector of values seen within the
|
cycle_labs |
Character column vector. Vector of labels to be mapped to
the associated |
summary_only |
Logical. Only display the summary measures in figures /
Suppress the individual time points from plotting. Defaults to
|
summary_highlight |
Logical. Add black box around summary measure bar
chart. Defaults to |
cycles_only |
Logical. Only display the longitudinal time points in
figures / Suppress the summary measures from plotting. Defaults to
|
x_lab_angle |
A integer between 0 and 360. Allows the user to rotate the
x axis labels in order to fit long arm names (0 or 45 recommended).
Defaults to |
x_lab_vjust |
A number. A ggplot2 object option. Allows the user to
vertically adjusts the x axis labels in order to fit arm names. Defaults to
|
x_lab_hjust |
A number. A ggplot2 object option. Allows the user to
horizontally adjusts the x axis labels in order to fit arm names. Defaults
to |
x_label |
A character string. Label for the x axis of the plot. Defaults
to |
y_label |
A character string. Label for the y axis of the plot. Defaults
to |
footnote_break |
Logical. Add a line break to the footnote Defaults to
|
suppress_legend |
Logical. Suppress the legend from appearing in figure.
Defaults to |
add_item_title |
Logical. Add the symptom item name as a title to the
figure. Defaults to |
Value
A list object. The returned object is a (k X 2) or (k x 3) nested list. Where k is the number of PRO-CTCAE item groups (e.g. pain, fatigue, nausea); list[[1 ... i ... k]]. For each list item there are 2 or 3 elements. The 1st element of each list item is the name of the PRO-CTCAE item group returned as a string. The 2nd element is the PRO-CTCAE figure as a ggplot object. These objects can be modified as such.
Examples
## Not run:
fig_acute = toxFigures(dsn = ProAE::tox_acute,
cycle_var = "Cycle",
baseline_val = 1,
arm_var = "arm",
id_var = "id",
x_lab_angle = -45,
x_lab_vjust = .3,
x_lab_hjust = .2,
colors = 2)
fig_acute[[1]]
## End(Not run)