Creates advanced raincloud plots with longitudinal connections using ggrain package. This module complements the existing Raincloud Plot module by providing advanced features including longitudinal data connections, Likert scale support, and flexible raincloud positioning. Perfect for repeated measures data, survey analysis, and complex distribution visualization in clinical research. Uses the ggrain package for enhanced customization and connectivity features.
Usage
advancedraincloud(
data,
y_var,
x_var,
fill_var = NULL,
id_var = NULL,
cov_var = NULL,
rain_side = "l",
likert_mode = FALSE,
show_longitudinal = FALSE,
point_size = 1.5,
point_alpha = 0.7,
violin_alpha = 0.7,
boxplot_width = 0.1,
jitter_seed = 42,
color_palette = "clinical",
plot_title = "Advanced Raincloud Plot",
x_label = "",
y_label = "",
show_statistics = TRUE,
show_comparisons = FALSE,
show_interpretation = TRUE,
clinical_cutoff = 0,
reference_range_min = 0,
reference_range_max = 0,
show_mcid = FALSE,
mcid_value = 0,
show_effect_size = FALSE,
effect_size_type = "cohens_d",
show_change_scores = FALSE,
baseline_group = "",
responder_threshold = 20,
show_sample_size = TRUE,
show_missing_info = FALSE,
trial_arms = "",
time_labels = "",
population_type = "itt",
log_transform = FALSE,
outlier_method = "none",
show_cv_bands = FALSE,
cv_band_1 = 15,
cv_band_2 = 20,
p_value_position = "above",
journal_style = "default",
generate_report = FALSE,
include_methods = FALSE
)Arguments
- data
The data as a data frame.
- y_var
Continuous variable for distribution visualization on Y-axis.
- x_var
Grouping variable for X-axis categories.
- fill_var
Optional variable for color filling different groups.
- id_var
Optional ID variable for connecting longitudinal observations across groups.
- cov_var
Optional variable for remapping point colors based on covariate values.
- rain_side
Position of the raincloud relative to the data points. Options include left (l), right (r), flanking both sides (f), 1x1 flanking (f1x1), and 2x2 flanking (f2x2).
- likert_mode
If TRUE, adds Y-axis jittering for Likert scale or ordinal data.
- show_longitudinal
If TRUE, connects repeated observations using the ID variable.
- point_size
Size of individual data points.
- point_alpha
Transparency level for data points.
- violin_alpha
Transparency level for violin plots.
- boxplot_width
Width of the boxplot component.
- jitter_seed
Random seed for consistent point jittering across plot updates.
- color_palette
Color palette for different groups.
- plot_title
Title for the raincloud plot.
- x_label
Custom label for X-axis. If empty, uses variable name.
- y_label
Custom label for Y-axis. If empty, uses variable name.
- show_statistics
If TRUE, displays summary statistics table.
- show_comparisons
If TRUE, performs statistical tests between groups.
- show_interpretation
If TRUE, displays interpretation and feature guide.
- clinical_cutoff
Add horizontal line for clinical threshold or decision boundary.
- reference_range_min
Lower bound of normal reference range (shaded area).
- reference_range_max
Upper bound of normal reference range (shaded area).
- show_mcid
Display Minimal Clinically Important Difference band.
- mcid_value
Size of the Minimal Clinically Important Difference.
- show_effect_size
Show effect size calculations between groups.
- effect_size_type
Method for calculating effect size.
- show_change_scores
Display change from baseline analysis for longitudinal data.
- baseline_group
Name or level of the baseline/reference group.
- responder_threshold
Percentage change threshold for responder classification.
- show_sample_size
Show sample size (N) for each group on the plot.
- show_missing_info
Display information about missing data and exclusions.
- trial_arms
Custom labels for treatment arms (comma-separated).
- time_labels
Custom labels for time points (comma-separated).
- population_type
Type of analysis population for clinical trials.
- log_transform
Apply log transformation to Y-axis values.
- outlier_method
Method for handling outliers in the data.
- show_cv_bands
Display coefficient of variation bands for assay variability.
- cv_band_1
First CV band percentage (typically 15\ variability).
- cv_band_2
Second CV band percentage (typically 20\ variability).
- p_value_position
Where to display p-values from group comparisons.
- journal_style
Apply journal-specific formatting guidelines.
- generate_report
Generate comprehensive clinical analysis report.
- include_methods
Include methods section text for publications.