Boxplot Function Enhanced for Specific Group Comparisons.

This function generates boxplots for each combination of numeric and factor variables in the provided data. Character columns are converted to factors and the function checks that the data contains at least one numeric and one factor column. If the scale argument is provided, numeric columns are transformed with the shared scaling helper before plotting. The function then creates boxplots using ggplot2 for each numeric variable grouped by each factor variable. If output_file is provided, the plots are saved to that PDF file; otherwise, a list of ggplot objects is returned.

Usage

cyt_bp2(
  data,
  output_file = NULL,
  mf_row = c(1, 1),
  scale = NULL,
  y_lim = NULL,
  progress = NULL,
  custom_fn = NULL
)

Arguments

data

A matrix or data frame of raw data.

output_file

Optional. A string representing the file path for the PDF file to be created. If NULL (default), the function returns a list of ggplot objects.

mf_row

A numeric vector of length two specifying the layout (rows and columns) for the plots in the PDF output. Defaults to c(1, 1). (Ignored when returning ggplot objects.)

scale

Transformation option for continuous variables. Options are NULL (default; no transformation), "none", "log2", "log10", "zscore", or "custom".

y_lim

An optional numeric vector defining the y-axis limits for the plots.

progress

Optional. A Shiny Progress object for reporting progress updates.

custom_fn

Optional transformation function used when scale = "custom".

Value

If output_file is NULL, returns a list of ggplot objects (named as "num_vs_factor" for each combination). If output_file is provided, a PDF file is created and the function returns NULL invisibly.

Examples

# Loading data
data_df <- ExampleData1[, -c(3, 5:28)]
data_df <- dplyr::filter(data_df, Group == "T2D", Treatment == "Unstimulated")
cyt_bp2(data_df, output_file = NULL, scale = "log2")
#> Warning: `cyt_bp2()` was deprecated in CytokineProfileShinyApp 0.0.1.
#> ℹ Please use `cyt_bp()` instead.
#> $IL.17F_vs_Group

#> 
#> $IL.17F_vs_Treatment

#>