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
)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 that the file extension matches the desired format (e.g., ".pdf" for PDF output or ".png" for PNG output or .tiff for TIFF output).- 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. Accepts "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 isFALSE.
