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Violin Plots for Continuous Variables with Optional Grouping

Source: R/cyt_violin.R
cyt_violin.Rd

cyt_violin produces violin plots for each numeric variable in data, optionally grouped by one or more categorical variables. When grouping is not specified, the function behaves similarly to cyt_bp but uses violins instead of boxplots and supports pagination via the bin_size argument. When grouping is provided, a separate violin is drawn for each level (or interaction of levels) of the grouping variables. Users may optionally overlay boxplots within each violin to visualize the median and interquartile range.

Usage

cyt_violin(
  data,
  output_file = NULL,
  group_by = NULL,
  bin_size = 25,
  y_lim = NULL,
  scale = c("none", "log2", "log10", "zscore", "custom"),
  custom_fn = NULL,
  boxplot_overlay = FALSE,
  font_settings = NULL,
  progress = NULL
)

Arguments

data

A matrix or data frame containing numeric and categorical variables.

output_file

Optional string specifying the name of the file to be created. When NULL (default), plots are drawn on the current graphics device. Ensure the file extension matches the desired format (e.g., ".pdf", ".png", ".tiff").

group_by

Optional character vector specifying one or more columns to use for grouping. If NULL (default) no grouping is applied.

bin_size

Integer. Maximum number of violins per page when grouping is not used. Default is 25, mirroring cyt_bp.

y_lim

Optional numeric vector giving y-axis limits for the plots. Applies to all plots.

scale

Character specifying a transformation for numeric variables. One of "none", "log2", "log10", "zscore", or "custom". When "custom", supply a function via custom_fn.

custom_fn

A user-supplied function to transform numeric columns when scale = "custom".

boxplot_overlay

Logical. When TRUE, a narrow boxplot is drawn inside each violin to summarize the median and quartiles. Default is FALSE.

font_settings

Optional named list of font sizes for supported plot text elements.

progress

Optional. A Shiny Progress object for reporting progress updates.

Value

Invisibly returns a list of ggplot objects. When output_file is provided, plots are written to the specified file.

Author

Shubh Saraswat

Examples

# Violin plots without grouping
cyt_violin(ExampleData1[, -c(1:3)], output_file = NULL, scale = "zscore")

# Violin plots grouped by Group with boxplot overlay
cyt_violin(ExampleData1[, -c(3, 5:28)], group_by = "Group",
           boxplot_overlay = TRUE, scale = "log2")