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Generate Violin Plots for Individual Genes

Source: R/IndividualGenes_Violins.R
IndividualGenes_Violins.Rd

This function creates violin plots of gene expression data with jittered points and optional faceting. It allows visualization of individual gene expression distributions across sample groups.

Usage

IndividualGenes_Violins(
  data,
  metadata = NULL,
  genes,
  GroupingVariable,
  plot = TRUE,
  ncol = NULL,
  nrow = NULL,
  divide = NULL,
  invert_divide = FALSE,
  ColorValues = NULL,
  pointSize = 2,
  ColorVariable = NULL,
  title = NULL,
  widthTitle = 16,
  y_limits = NULL,
  legend_nrow = NULL,
  xlab = NULL,
  colorlab = NULL
)

Arguments

data

A data frame containing gene expression values with row names as gene names and column names as sample IDs. (Required)

metadata

An optional data frame containing sample metadata. The first column must match the sample IDs from data. (Optional)

genes

A character vector of gene names to be plotted. (Required)

GroupingVariable

A character string specifying the column in metadata used for grouping samples on the x-axis. (Required)

plot

A logical value indicating whether to print the plot. If FALSE, only the output list is returned. Default is TRUE. (Optional)

ncol

An optional numeric value specifying the number of columns in the facet grid. If not provided, it is computed automatically. Only applicable if divide is NULL. (Optional)

nrow

An optional numeric value specifying the number of rows in the facet grid. If not provided, it is computed automatically. Only applicable if divide is NULL. (Optional)

divide

An optional character string specifying a column in metadata to be used for facetting, besides faceting by genes. (Optional)

invert_divide

A logical value indicating whether to invert the facet layout, when divide is being used. Default is FALSE, corresponding to genes in the rows. (Optional)

ColorValues

An optional named vector mapping unique values of ColorVariable to specific colors. If NULL, a default Brewer palette ("Paired") is used. (Optional)

pointSize

A numeric value specifying the size of the points in the plot. Default is 2. (Optional)

ColorVariable

A character string specifying a metadata column used for coloring points. Default is NULL. (Optional)

title

A character string specifying the title of the plot. Default is NULL. (Optional)

widthTitle

A numeric value specifying the maximum width of the title before inserting line breaks. (Optional)

y_limits

A numeric vector of length 2 specifying the limits of the y-axis. If NULL (default), the y-axis is adjusted automatically. (Optional)

legend_nrow

A numeric value specifying the number of rows in the legend. Default is NULL. (Optional)

xlab

A character string specifying the x-axis label. If NULL, it defaults to GroupingVariable. (Optional)

colorlab

A character string specifying the legend title for colors. Default is an empty string. (Optional)

Value

A list containing:

plot

A ggplot2 object representing the facetted violin plots.

data

A data frame used for plotting, including transformed expression values (log2) and metadata.

Details

The function processes the gene expression data, filters for the specified genes, and transforms expression values using log2(). A violin plot with jittered points is generated using ggplot2. A median summary is added as a crossbar. If divide is provided, facets are created using ggh4x::facet_grid2(). Color customization is available via ColorVariable and ColorValues.

Examples

# Example dataset
data <- data.frame(
  A = c(10, 20, 30),
  B = c(5, 15, 25),
  C = c(2, 12, 22)
)
rownames(data) <- c("Gene1", "Gene2", "Gene3")

metadata <- data.frame(
  sample = c("A", "B", "C"),
  Group = c("Control", "Treatment", "Control")
)

genes <- c("Gene1", "Gene2")

IndividualGenes_Violins(data, metadata, genes, "Group")
#> Using gene as id variables
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.