rna.plot_bar: Plot bar plots for gene abundance or fold change

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Plot bar plots for gene abundance or fold change

Description

This function generates bar plots for gene abundance or fold change, normalized by either a reference gene or centered to the mean. The user can also plot the contrast of two conditions.

Usage

rna.plot_bar(
  dds,
  genes,
  type = c("contrast", "centered"),
  shrunken.lfc = T,
  contrast = NULL,
  col.id = "ID",
  name_table = NULL,
  match.id = "Accession",
  match.name = "Name",
  convert_name = FALSE,
  shape.size = 2.5,
  collage = TRUE,
  plot = TRUE,
  export = TRUE,
  export.nm = NULL
)

Arguments

dds	A DESeqDataSet object containing the data.
genes	A vector of gene names or IDs.
type	Type of plot: "centered" or "contrast".
shrunken.lfc	A logical indicating if shrunken log2 fold changes should be used if type = "contrast". Default is TRUE.
contrast	Name of the contrast for plotting when type is "contrast".
col.id	Name of the column with gene IDs in dep.
name_table	A data frame containing the mapping of gene names to reference names.
match.id	The name of a column in name_table to find matches with col.id.
match.name	The name of a column in name_table to assign new names based on matches of col.id and match.id.
convert_name	Logical value indicating whether to convert the gene names to reference names based on name_table (e.g., gene names).
shape.size	Numeric value defining the (replicate) symbol size in the plot
collage	A logical indicating if multiple plots for different genes should be combined into collages of up to 8 plots. Default is TRUE.
plot	wether to return the plot or not.
export	Logical; whether to export the plot as PDF an PNG files
export.nm	Name of the output PDF and PNG files if export = TRUE.

Value

If plot is set to FALSE and the length of genes is less than or equal to 8, a data frame with the log2 fold changes or log2 intensities, along with their lower and upper bounds of 95% confidence intervals, is returned.

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.