CytoProfile (version 0.2.4)

cyt_bp: Boxplots for Continuous Variables with Optional Grouping

Description

This function generates boxplots for numeric variables in a data frame or matrix. It supports optional grouping by one or more categorical variables. Numeric variables can be scaled using various transformations before plotting. When grouping is not used, boxplots are arranged in pages with a specified maximum number of plots per page. Plots can be saved to a PDF file or displayed on the current graphics device.

Usage

cyt_bp(
  data,
  output_file = NULL,
  group_by = NULL,
  bin_size = 25,
  y_lim = NULL,
  scale = c("none", "log2", "log10", "zscore", "custom"),
  custom_fn = NULL
)

Value

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

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 boxplots per page when grouping is not used. Default is 25, as in the original 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".

Examples

data("ExampleData1")
# Boxplots without grouping
cyt_bp(ExampleData1[, -c(1:3)], output_file = NULL, scale = "log2")
# Boxplots grouped by Group
cyt_bp(ExampleData1[, -c(3,5:28)], group_by = "Group", scale = "zscore")