toxFigures: Create PRO-CTCAE severity frequency distribution figures for...
In blakelanglais/ProAE: PRO-CTCAE Scoring, Analysis, and Graphical Tools

Description Usage Arguments Value Examples

Data format should be in 'long' format, where each PRO-CTCAE item is a variable/column.

toxFigures(
  dsn,
  id_var,
  cycle_var,
  baseline_val,
  arm_var = NA,
  plot_limit = NA,
  colors = 1,
  label = 0,
  summary_only = FALSE,
  cycles_only = FALSE,
  x_lab_angle = 0,
  x_lab_vjust = 1,
  x_lab_hjust = 0,
  x_label = "Randomized Treatment Assignment",
  plot_data = FALSE
)

`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 `NA`.
`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 `NA`.
`colors`	A number. Specify the coloring scheme of symptom grades 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.
`label`	A number. Label frequency bars with sample size (n) or percent shown on the y-axis. Label options include: `1` = sample size (n) within each cycle (symptom grade 0 or higher), `2` = sample size (n) within each cycle with present symptoms (symptom grade > 0), `3` = sample size (n) within each cycle with severe symptoms (symptom grade >= 3), `4` = percent of subjects within each cycle with present symptoms (symptom grade > 0), `5` = percent of subjects within each cycle with severe symptoms (symptom grade >= 3). No labels will be applied if not specified. Defaults to `NA`.
`summary_only`	Logical. Only display the summary measures in figures / Suppress the individual time points from plotting. Defaults to `FALSE`.
`cycles_only`	Logical. Only display the longitudinal time points in figures / Suppress the summary measures from plotting. Defaults to `FALSE`.
`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 `0`.
`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 `1`.
`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 `0`.
`x_label`	A character string. Label for the x axis of the plot. Defaults to `"Randomized Treatment Assignment"` if `arm_var` is specified, defaults to `"Overall"` if not `arm_var` is specified.
`plot_data`	Logical. Return the data used to construct plots as element of the returned object. Defaults to `FALSE`.

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. The 3rd (and optional) element is the data used to construct the ggplot figure, available via plot_data.

fig_acute = toxFigures(dsn = ProAE::tox_acute[c(1:300, 1101:1400),],
 cycle_var = "Cycle",
 baseline_val = 1,
 arm_var = "arm",
 id_var = "id",
 label = 0,
 x_lab_angle = -45,
 x_lab_vjust =  .3,
 x_lab_hjust = .2,
 colors = 2)
fig_acute[[1]]