Creates publication-ready plots with GraphPad Prism styling using ggprism package. This module provides Prism-style themes, color palettes, and statistical annotations to create professional scientific visualizations. Perfect for clinical research publications, biostatistics, and academic presentations. Supports various plot types including violin plots, box plots, scatter plots, and dose-response curves with seamless ggplot2 integration and Prism-style aesthetics.
Usage
ggprism(
data,
x_var,
y_var,
group_var,
facet_var,
plot_type = "violin",
prism_theme = "default",
prism_palette = "floral",
show_points = TRUE,
point_size = 1.5,
point_alpha = 0.6,
show_statistics = TRUE,
stats_method = "auto",
pvalue_format = "exact",
plot_title = "GraphPad Prism Style Plot",
x_label = "",
y_label = "",
legend_position = "right",
base_size = 12,
show_summary = TRUE,
error_bars = "se",
prism_guides = "standard",
annotation_ticks = FALSE,
preview_mode = FALSE,
prism_shape_palette = "default",
jitter_width = 0.2,
violin_width = 1,
publication_ready = FALSE,
export_dpi = 300,
custom_comparisons = ""
)Arguments
- data
The data as a data frame.
- x_var
Variable for the X-axis. Can be continuous or categorical.
- y_var
Continuous variable for the Y-axis.
- group_var
Optional categorical variable for grouping and statistical comparisons.
- facet_var
Optional variable for creating separate panels in a grid layout.
- plot_type
Type of plot to create with Prism styling.
- prism_theme
GraphPad Prism theme variant to apply.
- prism_palette
Prism-style color palette for different groups. Choose from 20+ authentic GraphPad Prism palettes.
- show_points
If TRUE, overlays individual data points on the plot.
- point_size
Size of individual data points.
- point_alpha
Transparency level for data points (0 = transparent, 1 = opaque).
- show_statistics
If TRUE, performs statistical tests and adds p-value annotations.
- stats_method
Statistical test method for group comparisons.
- pvalue_format
Format for displaying p-values in statistical annotations.
- plot_title
Custom title for the 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.
- legend_position
Position of the legend in the plot.
- base_size
Base font size for all text elements in the plot.
- show_summary
If TRUE, displays summary statistics table.
- error_bars
Type of error bars to display (for applicable plot types).
- prism_guides
Axis guide style following GraphPad Prism conventions.
- annotation_ticks
Add tick marks as annotations in Prism style.
- preview_mode
Enable palette preview mode to see all colors in the selected palette.
- prism_shape_palette
Shape palette for point plots following Prism conventions.
- jitter_width
Width of horizontal jittering for overlaid points.
- violin_width
Scale factor for violin plot widths.
- publication_ready
Optimize plot for publication with enhanced styling and formatting.
- export_dpi
DPI for high-resolution export (publication standard: 300).
- custom_comparisons
Custom pairwise comparisons (e.g., "Group1-Group2,Group1-Group3").
Value
A results object containing:
results$instructions | a html | ||||
results$main_plot | an image | ||||
results$palette_preview | an image | ||||
results$publication_plot | an image | ||||
results$summary_statistics | a html | ||||
results$statistical_tests | a html | ||||
results$prism_guide | a html | ||||
results$palette_information | a html | ||||
results$export_code | a html | ||||
results$accessibility_notes | a html |
Examples
# \donttest{
# Example:
# 1. Load your data frame with continuous and categorical variables.
# 2. Select variables for X and Y axes.
# 3. Choose grouping variables for statistical comparisons.
# 4. Customize with Prism-style themes and color palettes.
# 5. Add statistical annotations and publication formatting.
# }